sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b69b2765f9736a810b79ddeb8309f68b95256d785dea6a6a6f2f1e21179c1389 | Python | 7,940 | 178 | from .vehicle_wheel_smoke_test import VehicleWheelSmokeTest
import carla
import math
ANGLE_TOLERANCE_DEG = 2.0
OFFSET_TOLERANCE_M = 0.01
STEER_DEG = 20.0
PITCH_DEG = 45.0
SUSPENSION_M = 0.05
WHEELS = (
carla.VehicleWheelLocation.FL_Wheel,
carla.VehicleWheelLocation.FR_Wheel,
carla.VehicleWheelLocation.B... |
4f7005b8517ae72c19abc681d8fac4f59400d7a4d8f33953bd97a85db631958c | Python | 7,941 | 140 | __author__ = 'duarte'
from modules.parameters import ParameterSet, 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 single_... |
8d09c1d00e0d41b76feecacb22d6b7d50c929901bde75484078fad55b8bbc60c | Python | 7,945 | 208 | #!/usr/bin/env python3
"""Author and validate a <Name>.Package.json for a CARLA standalone asset package.
PrepareAssetsForCooking locates the file by RECURSIVE SEARCH under
Unreal/CarlaUE4/Content, so the package name is just the filename minus
".Package.json" — no matching directory is required. That is what lets sto... |
4e0799ebf70fe8ce5de3710664790968b3742e6063a0abfdd3b9957614c91ebe | Python | 7,946 | 188 | """ Module including helper functions for feature extraction and other stuff including metrics, jsonhandler, etc"""
import json
from collections import Counter
import logging
import re
import numpy as np
import string
logger = logging.getLogger('classifier')
regex_find_citation = re.compile(r"\(\s?(([A-Za-z\-]+\s)+([... |
451914de4a1fa1bb0756fd7874b77b1617a1367d6234b49efda710968956087e | Python | 7,950 | 198 | """
MODULE VERSION:
Create peptide GRO and ITP from an amino acid sequence and an ssdump secondary structure.
"""
import subprocess
import shutil
import os
import core.settings as CoreSettings
import core.system as System
import core.gromacs as Gromacs
import core.gromacs_commands
import user.usersettings as UserSet... |
8d6831936d8eebb986d2f92fa7718dd4da549eb860418e559a1bd60993ea45a5 | Python | 7,951 | 201 | # 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... |
3d5035a6d25c65cf9adce13b8d41e82dedc816e7c9129ae5d4d9c24f714a8ab4 | Python | 7,954 | 138 | #%%
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 = pymaid.CatmaidInstance(url, token, name, password)
import connectome_tools.cluster_analysis as clust
import connectome_tools.celltype as ct
import con... |
2bd044146a3de19e68c2df43f617164519058c385146c6fb02920f219450c4e6 | Python | 7,967 | 224 | import unittest
import numpy as np
from grr.ThresholdModel import constructMedianModel
from grr.ModelStimulus import ModelStimulus
from ezephys import stimtools
class TestSimulateDoesNotCrash_VectorInput(object):
def setUp(self):
self.dt = 0.1
self.V0 = -70.0
self.spkTimes = [50.0, 700.0... |
d91b017eaaba961da588326c5784b3316938d6695ac7af02573e586cab1ef6e4 | Python | 7,969 | 300 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.stats import poisson
from graspy.embed import OmnibusEmbed, selectSVD
from graspy.match import GraphMatch
from graspy.models import DCSBMEstimator... |
a849541afbe64c02252f11bee02e107d5000dc8c6b8b219f48c8ff12d482b9b2 | Python | 7,971 | 195 | """
File: create_cov_matrices.py
Created: 2020/03/12
Last Changed: 2020/06/03
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... |
cc72291b2895db7aa37d5a93ce72368ff45e75b095812cc32bb0d84f9f5e762a | Python | 7,978 | 201 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
eb584a4cf28d56cd8afea10f7cfe566d40fa6733336b006f09d07ea8c4a21069 | Python | 7,982 | 230 | # System libs
import os
import time
import argparse
from distutils.version import LooseVersion
# Numerical libs
import numpy as np
import torch
import torch.nn as nn
from scipy.io import loadmat
import torch.utils.data as data
import nibabel as nib
# Our libs
from data.augmentations import ComposeTest, PaddingCenterCro... |
26de722d723361d0057d8eb977fd032fc2f2fd9434c84adbb2cf0426bd5b5df9 | Python | 7,986 | 176 | # 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... |
202ae7bd9df7f1b23bf4a452f1c5691176d51ec170bdcd097b400fce3845c744 | Python | 7,987 | 244 | import numpy as np
import logging
from scipy.special import lpmv, gammaln
from tqdm import tqdm
import math
from dipy.reconst.gqi import squared_radial_component
from dipy.data import default_sphere
from dipy.tracking.streamline import set_number_of_points
from scipy.linalg import blas
logger = logging.getLogger(... |
3972cce0f8e4b67e14e68ea465a7496efa23456e02ad70810c563ae3445e9c4d | Python | 7,987 | 287 | #%%
from itertools import chain
from pathlib import Path
from giskard import graph
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.colors import ListedColormap
from matplotlib.lines import Line2D
from sklearn.metrics import pairwise_distances
from src.data ... |
57df1595d09d0bcea451a16203b6424ad4a13bc9f58aa2f83451f0dd65cc5743 | Python | 7,992 | 297 | import numpy as np
from collections import namedtuple
from scipy import stats
from scipy import optimize
import statsmodels.api as sm
import statsmodels.formula.api as smf
from sklearn.decomposition import FastICA
GroupStats = namedtuple("GroupStats",
["xs", "centers", "ns", "lowerbnds", "uppe... |
f9f1fc5f02d262efa003f122fbdc0b7081c1de5504e126a8c95398b6c5567a88 | Python | 7,993 | 192 | """
File: main.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, either version 3 ... |
44867aab3092627acdaa829461106f27df714d55158e017ab4ad8df4d6b35de9 | Python | 7,997 | 145 | # %%
# generate cascades from individual neuron pairs and individual nonpaired neurons
from data_settings import data_date, pairs_path
from pymaid_creds import url, name, password, token
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
import numpy as np
import pandas as pd
import pickle
from co... |
203a3e9e28696816ffaab8260707accf7e27437017fd3ff93a64f8e7007d2959 | Python | 7,998 | 221 | import os
import sys
import numpy as np
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtCore import *
import pyqtgraph as pg
from .uuuuuu import read_qss_file
reset_button_style = '''
QPushButton{
background: #656565;
border-radius: 5px;
color: white;
border-style: outset;
bor... |
d65c8e4f004a9759497b643480644d060f5dbc223887585aa7e054c3ed84de7e | Python | 7,999 | 182 | #!/usr/bin/env python3
"""Check a file is a usable input for the walker pipeline — the FIRST thing to run.
python3 check_input.py ~/models/SK_MyPed.fbx
Four gates, cheapest first, no editor involved (well under a second):
1. FORMAT it must be an FBX. Unreal imports FBX; .ma/.mb/.blend/.max/.c4d and
... |
4443d66abd0acb8c4d1eb81a4a31be2cd6aad034c242211de368c0c9b898eaa4 | Python | 8,004 | 250 | # 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 re
import pickle
import random
import inspect
import argparse
import subprocess
import torch
from torch import... |
58d4ed08f94f339eb2f736df392f9f4c37b16c87a8d9bdb88a85d7a7c64befe0 | Python | 8,005 | 230 | #!/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... |
cf3688290f54e59442ce18c4a352e22e7a924b70624199326b25cee3fb413505 | Python | 8,008 | 195 | from Lif_Parameters import *
from Lif_Equations import eqs_LIF
seed(val)
#####################################
# Initialize the neuronal populations - SX
#####################################
# ------- Layer 0 -------
# l0 = NeuronGroup(2*n_cells, eqs_LIF, method='exponential_euler', threshold='vm>v_th', reset='vm=v_r'... |
7f8abf0eb3cd3605ca29059a2e6ee4eedff0d9a129d9e4a45592f17d210808d4 | Python | 8,009 | 215 | from Bio.PDB import *
import numpy as np
from sklearn.neighbors import KDTree
"""
computeCharges.py: Wrapper function to compute hydrogen bond potential (free electrons/protons) in the surface
Pablo Gainza - LPDI STI EPFL 2019
This file is part of MaSIF.
Released under an Apache License 2.0
"""
from default_config.ch... |
617ce0599a61d059789b6f73c45b7722f5b569d16bd9f3f2b46b019fb270f55a | Python | 8,011 | 224 | """Discrimators used in pi-GAN"""
import math
import torch
import torch.nn as nn
import sys
# sys.path.append('/apdcephfs/share_1330077/starksun/projects/pi-GAN')
import curriculums
import numpy as np
import torch.nn.functional as F
from discriminators.sgdiscriminators import *
# from sgdiscriminators import *
class... |
8d845d83124f411159533e6184beda052635b894d0f35f69584d0133b2841a1b | Python | 8,011 | 203 | # 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... |
9329a84969840069ca90fc7676ffc2cdb8bcdfb80f40f908e9e3e1f3e0a343c7 | Python | 8,012 | 236 | from copy import deepcopy
import networkx as nx
import numpy as np
import pandas as pd
from graspologic.utils import largest_connected_component
from .utils import get_paired_inds, to_pandas_edgelist
class MaggotGraph:
def __init__(self, g, nodes=None, edges=None):
self.g = g
# TODO add checks ... |
dbfbfc49e9482d8d206f8100081c51cb56aa0e7630d0468a736c83c8c29f06d4 | Python | 8,012 | 201 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
35cbc49f3ec89a586b6d9162a3913961075401ccd2f2a3b19ef3d13b66ddabfe | Python | 8,015 | 206 | ####################################################################################################
# Copyright (c) 2019, 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 softwar... |
e177dd7799769e38bf1e0846e10aa683d4dd79d785fa6047e7c0c418cf244af9 | Python | 8,015 | 239 | ################################
### Module to write the slurm files for the supercomputer
##################################
def get_slurmtemplate (jobname,templatefile='../src/io/template.slurm'):
with open(templatefile, 'r') as f:
slurm_template=[]
slurm_template+='#!/bin/bash\n'
... |
f2da411e5e32ea5ef983373a173db76eacd2f66285849c03c833c6d7f6a1f32a | Python | 8,017 | 155 | import numpy as np
from nipype import Workflow, Node, MapNode, IdentityInterface
from nipype.interfaces.fsl import maths, BET, MCFLIRT, ExtractROI, FLIRT, Merge, ApplyXFM, ImageMaths, BinaryMaths, ConvertXFM
from nipype.interfaces.ants import Registration, ApplyTransforms
import nipype.interfaces.utility as util
from q... |
ba907997ff69687340478eff3da33e1a1abc67fa3da29341d0a66fbaeeb32090 | Python | 8,019 | 190 | """Public-API and CLI regressions for empty alignment tracks (#808)."""
import subprocess
import sys
import pytest
from conftest import macs3_env
from test_Parser_bam_truncation import write_bam
from test_Parser_bampe_validation import HEADER, alignment
TRACK_PROBE = '''
import numpy as np
from MACS3.Signal.Paired... |
8bef5101505512aee5231add02085803eac13e5fb87027ef953d7756e32990f2 | Python | 8,026 | 193 | import unittest
import kgcl_schema.grammar.parser as kgcl_parser
import yaml
from linkml_runtime.dumpers import yaml_dumper
from oaklib import get_adapter
from oaklib.datamodels.cross_ontology_diff import DiffCategory, RelationalDiff
from oaklib.datamodels.vocabulary import HAS_PART, IS_A, PART_OF
from oaklib.impleme... |
ca5f2fbce706df601dccd6db344282d2cfdec895ccb57c135b64596a240ebf6e | Python | 8,028 | 197 | import sys
import numpy as np
import pandas as pd
import networkx as nx
import time
from tqdm import tqdm
sys.path.append(".")
from lib import skel
from lib import string2list as s2l
# Define volume properties
xres = yres = 3.58 # in nm/px
zres = 40
# Get all pyramidal and interneuron segment IDs
# These are the I... |
25bf2b982dda9ee24d1635889ca33dec923249a511092094295801f140e88930 | Python | 8,034 | 239 | ####################################################################################################
# Copyright (c) 2016 - 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
27f2b738c1a4ea778463424b076b7ec1615ef4f13da56ee17e647869cc2d2d18 | Python | 8,034 | 250 | """
Training script for Burgers equation using the Recurrent Neural Operator (RNO).
This script trains an RNO on the 1D time-dependent Burgers equation
using a small in-repo dataset.
"""
import sys
from pathlib import Path
import torch
import wandb
import torch.nn as nn
from zencfg import make_config_from_cli
# Ad... |
9546a7f36fd1d103c497e5cc412783ee081368997e67ee24ecefbf4220e63359 | Python | 8,036 | 159 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 1 11:58:30 2021
@author: paulmueller
This script reads all header files of a patient, looks for corresponing VI files.
It creates a new DataFrame which has all VI values but excludes seizures already.
The DataFrame has the columns:
index(time... |
647c7624e21102f24cab2a07126b83809a36d294060d4f8e1d9f5c2f10117a93 | Python | 8,037 | 201 | # 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... |
b51d55c2373597a15997ca9197fb744d865855423fa73d44f5aede0b8e1864bf | Python | 8,037 | 190 | # 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... |
3d390f010745854208af803b3c7bd2fc8ed3f166f5ab67057edc8aee0a5baa23 | Python | 8,039 | 145 | from functions import *
import numpy as np
import matplotlib.pyplot as plt
import pickle
from itertools import starmap
from operator import mul
starttime = datetime.now()
GiacoPath = "./28nets_rules/Giacomantonio2010.txt"
#Averages of Distributions to be plotted as dashed vertical lines
def avgOfDistr(distr):
#St... |
890db4e2345df2ff75651c5d327632270ceba56ddfbf6149ec320a599d3d0634 | Python | 8,041 | 206 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
import warnings
import pandas as pd
from Bio import BiopythonWarning
from Bio.PDB import *
from tmkit.base import PDB
from tmkit.sequence i... |
937f93c1c058e517267e1d606cc22e83ab906844c62b0b46367815a9e121e978 | Python | 8,041 | 191 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
88336dcf53279c9ccee2fbf94c529bc24df82cbd84daf9d544f0677ee47c3746 | Python | 8,042 | 191 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
a1cbdb92f38e4eff9d051c115a4959994d1e71f312f0cc51e265012273d89ed0 | Python | 8,042 | 192 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
aea19e867dd34f7668a0697c26238a06835e206d08ad39e5ed4bfc96f08f38c9 | Python | 8,042 | 231 | """
This module provides the `MultiFileSampler` class, which uses a
FileSampler for each mode of sampling (train, test, validation).
The MultiFileSampler is therefore a subclass of Sampler.
"""
from .sampler import Sampler
class MultiFileSampler(Sampler):
"""
This sampler contains individual file samplers fo... |
29448b18264418682b84b5e74a86bec3f4af67e3dbe52b8ebfca19156b70c30a | Python | 8,043 | 207 | #!/usr/bin/env python
import os
import json
import math
import argparse
import pandas as pd
from drugex.data.corpus.vocabulary import VocGraph, VocGPT, VocSmiles
from drugex.data.datasets import GraphFragDataSet, SmilesFragDataSet
from drugex.data.utils import getVocPaths
from drugex.logs.utils import enable_file_logg... |
3bdb89fc68e047cd9c19cf6456be78e80c4784f7e08631cf4603cd7e52bf638a | Python | 8,043 | 186 | # 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... |
625240db22187e3640ca4ab11503e2a247d64429c3f44941a1e65969c1cad768 | Python | 8,043 | 201 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
18657b084d9df0a18f125d35b15c08a1a3a93e3f77aa59480239bc6fdad05b06 | Python | 8,046 | 244 | #!/usr/bin/env python3
"""
Based on
https://github.com/BIDS-Apps/example/blob/aa0d4808974d79c9fbe54d56d3b47bb2cf4e0a0d/run.py
"""
import argparse
import os
import os.path as op
def get_parser():
parser = argparse.ArgumentParser(description="Run MRIQC on BIDS dataset.")
parser.add_argument(
"-b",
... |
1395871266bd7776e26c1a616ce9e3815e6db249b3d185535f453ad046651357 | Python | 8,049 | 262 | import numba
import numpy as np
import pandas as pd
from numba import prange
@numba.jit(parallel=True, nopython=True)
def avg_da(data, time, start, stop):
inds = (time >= start) & (time <= stop)
tmp = data[:, inds]
mu = np.zeros(len(tmp))
for i in prange(len(mu)):
mu[i] = np.nanmean(tmp[i])
... |
25f033213ece1c5155c4b057de2ed0085154e13119fb76a7228b13f92d2e4fb5 | Python | 8,053 | 223 | import sys
import pandas as pd
import numpy as np
import os
from itertools import groupby
import utils.general_utils as general_utils
import utils.plot_utils as plot_utils
import utils.plot_setting as plot_setting
import utils.math_utils as math_utils
import utils.sync_utils as sync_utils
import utils.list_twoP_exp a... |
affffca7bedab4bfca9b8a005c31afb9448b05a6873ffb636e1a22c552e0744c | Python | 8,055 | 232 | from typing import List, Union
from pathlib import Path
import numpy as np
import torch
from torch.utils.data import DataLoader
from neuralop.data.transforms.data_processors import DataProcessor
from .dict_dataset import DictDataset
from ..transforms.normalizers import UnitGaussianNormalizer
from .ot_datamodule impo... |
d964425ede8d6a568d52403d107795d9024a4351772c8c0fe1baba6d96f00f15 | Python | 8,055 | 234 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Any, Optional
import subprocess
import numpy as np
import pandas as pd
from tmkit.util.Kit import chainid, tactic5, tac... |
d68b8b074465a34eb925836870344c7b66117068df5cb55a2dfd3a1aa83f80ae | Python | 8,056 | 215 | import logging
import numpy as np
from utime.sequences.base_sequence import _BaseSequence
from psg_utils.errors import NotLoadedError
logger = logging.getLogger(__name__)
def _assert_comparable_sequencers(sequencers):
"""
Takes a list of utime.sequencer Sequence objects and compares them for
equality on ... |
17854df504878c69bd1a2987db41350a2d67eda3b6f2ff7335979a9ecb83102f | Python | 8,058 | 208 | import logging
import sys
import warnings
from dataclasses import asdict
from functools import partial
import chika
import numpy as np
import pandas as pd
from fastai.callback.tracker import SaveModelCallback
from imblearn.metrics import geometric_mean_score
from sklearn.metrics import accuracy_score, cohen_kappa_scor... |
361d91f6e2d836c5f594ac22ff9ef104a662edd278f6f79101eef8dd9b4c578c | Python | 8,058 | 248 |
import cv2
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import numpy as np
from datetime import datetime
class ReferenceDialog(QDialog):
def __init__(self, Parent):
QDialog.__init__(self, Parent)
self.Form = Parent
class SnapshotDialog(QDialog):
def __... |
a5520d6a093d488b8e72f3a2c6197afdd797090c7c5fc468fdd1ff1472507f46 | Python | 8,064 | 209 | #!/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>.
"""Smooth movement of a camera interpolating collection of keypoints provided... |
d9a659c76ec82e7f3e63c5fd711ba18ec1f8c85c7f03efdbbb8a877595f8a479 | Python | 8,065 | 192 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
6e8c23e0ca3c3b411033161e450279a197f466542e427cfd8fde815b12a82ca5 | Python | 8,070 | 156 |
feature_filter = [
6452745, # 1.1.Goal setting (behavior)
6452746, # 1.2 Problem solving
#6452747, # 1.3 Goal setting (outcome)
6452748, # 1.4 Action planning
#6452749, # 1.5 Review behavior goal(s)
#6452750, # 1.6 Discrepancy between current behavior and goal
#6452751, # 1.7 Review outcome... |
8b599baf1f7aa3fe0573875daa8c5863874f36fc0f7a3aa4faea303f1b7dedeb | Python | 8,070 | 223 | """
Basic differential evolution implementation for RACCOON
F. Comitani @2019-2022
Based on
https://nathanrooy.github.io/posts/2017-08-27/simple-differential-evolution-with-python
Storn, R.; Price, K. (1997). "Differential evolution - a simple and efficient heuristic
for global optimization over continuous spaces... |
9b54f7aea4cdbaac3b142f3953daabf38f653d6f48795b90572800ad0351bf80 | Python | 8,072 | 247 | # LZW Update May 2017, Feb 12 2017 to match TN00344.
# G. Ruffini with Eleni Kroupi / Starlab + Neuroelectrics (2017)
# Updated May 2017 with Entropy rate calculators
# Part of this code from sources as indicated, but modified to
# be used with binary data.
# Permission is hereby granted, free of charge, to any pers... |
3b78bd5c630d6c1defc3019862f0c0fc3eafbea110cf75d502b6159bd30c9225 | Python | 8,077 | 202 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
ad9911bdac3de20cf14213b33d1fe0217a785d545b197bbb844aa2769170a77d | Python | 8,078 | 246 | """
Tools for loading data from text files.
.. autosummary::
:toctree: generated
tsv
var
"""
import csv
import os
import re
from typing import Sequence, Union
import numpy as np
from .._utils import ui
from .._utils.parse import FLOAT_NAN_PATTERN
from .. import _data_obj as _data
__all__ = ('tsv', 'var')
... |
ea94fcecaf8d57fba5a822825494e11b8843ba0dfc743872c83e4c800c9562b4 | Python | 8,078 | 200 | # 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... |
eb409dee10ec5ca87bfdac7a6a42328442f8b38c3371f8501b229e374f87b0f8 | Python | 8,080 | 194 | import sys
import time
import os
import logging
import argparse
import pysam
import cv2
from multiprocessing import Pool
from cnnLSV_combine import combine
from cnnLSV_encode import *
from cnnLSV_net import pre_sv
def parseArgs(argv):
parser = argparse.ArgumentParser()
parser.add_argument('bam'... |
14416d0ea0875003fa4f117beb7c4aa27e2c65239c2df8e1667b214593b3a821 | Python | 8,082 | 201 | import os
import collections
from os.path import join
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
274926a74c461b0cdd9e7539b058b8410c543a3ee8438d4ce174873e64f89140 | Python | 8,085 | 207 | import math
import torch
from torch.optim.optimizer import Optimizer, required
class RAdam(Optimizer):
def __init__(self, params, lr=1e-3, betas=(0.9, 0.999), eps=1e-8, weight_decay=0):
defaults = dict(lr=lr, betas=betas, eps=eps, weight_decay=weight_decay)
self.buffer = [[None, None, None] for in... |
2f16ef7538b7a30fae76703b919e4d23ad7c29c539ea352afe3f5d3503cd2059 | Python | 8,085 | 182 | """Public text-parser and bounded CLI regressions for #811 / #757 item 14."""
import gzip
import subprocess
import sys
import pytest
from conftest import macs3_env
HEADER = b'@HD\tVN:1.6\n@SQ\tSN:chr1\tLN:1000000\n@PG\tID:bwa\tPN:bwa\n'
SAM = (b'r1\t0\tchr1\t101\t60\t25M\t*\t0\t0\t' + b'A' * 25 +
b'\t' + b'... |
edd7091cf6781c908d6ff9ed85bd86f4ff3a07bc083046463fa9d5045d68343b | Python | 8,085 | 192 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
88c6e470fa387184cf07419d4577b90eb464744eb9e5bcd3d6a4ed7c658ed13a | Python | 8,089 | 240 | """
Extract summary stats about multiple simulations at once
"""
from tqdm.auto import tqdm as pbar
import numpy as np
import pandas as pd
from tctx.networks.turtle_data import DEFAULT_ACT_BINS
import logging
def extract_spike_counts_per_ei_type(cells, spikes, wins: pd.DataFrame):
"""
count number of spikes ... |
b7f02b2cc742454b8217027e6315507611e64927d4659673fceaec40319ceb87 | Python | 8,093 | 241 | # Copyright 2021 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... |
c11ddbd9cbc43b6b90d975d4461804fa6000f27b6ae4fd8d6c55be63ff33fe0d | Python | 8,096 | 208 | ####################################################################################################
# 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 ... |
8d6d6807eee01b6edee480406829c48fe6cf506dafa9b447aa19f37a513e53d3 | Python | 8,097 | 176 | import numpy as np
import torch
import torch.utils.data as data
from utils import coco
import utils
import json
with open("data/preprocess/coco_contexts_hard.json", "r") as read_file:
coco_contexts_hard = json.load(read_file)
possible_ctx_ids_hard = [ctx['cluster_ids'] for ctx in coco_contexts_hard]
with o... |
728fab941797378004c46ea3e0c561569a65f5db13a23f3617e5697e4fc17e96 | Python | 8,099 | 214 | # A modification version from chainercv repository.
# (See https://github.com/chainer/chainercv/blob/master/chainercv/evaluations/eval_detection_voc.py)
from __future__ import division
import os
from collections import defaultdict
import numpy as np
from maskrcnn_benchmark.structures.bounding_box import BoxList
from m... |
6f099a3e76800c2b433581bf4a571d8b04120f0f0c4a260cb473d0ade89d6a92 | Python | 8,100 | 203 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
d4dc4d8c5ec223f587ae66d7b609f921a348d48222eabbb86ac70d99ddcee31d | Python | 8,101 | 195 | # 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... |
f47cb4559a487ca5795084b60ae70b34e30273dfa010fa8f62dbb74556665d99 | Python | 8,104 | 236 | import torch
import numpy as np
import pickle
from scipy.ndimage import gaussian_filter1d
from util.datasets import Augmentations
FRAME_WIDTH_TOP = 144
FRAME_HEIGHT_TOP = 144
RESIDENT_COLOR = 'lawngreen'
INTRUDER_COLOR = 'skyblue'
class AllRandomAugmentations(Augmentations):
'''Applies a series of random augme... |
cebc6987761995b78a3d639a53c2890a37c865f262b794a2ba62db4874f45457 | Python | 8,106 | 183 | import numpy as np
from PIL import Image
from torch.utils.data import Dataset
from torch.utils.data.sampler import BatchSampler
class SiameseMNIST(Dataset):
"""
Train: For each sample creates randomly a positive or a negative pair
Test: Creates fixed pairs for testing
"""
def __init__(self, mnis... |
f67fcb2ef3c7c2911efff10f6fe595600e0c3e913dc47fa278da1f9180375e9d | Python | 8,106 | 225 | """
File: data_preprocessor.py
Created: 2020/06/29
Last Changed: 2021/08/04
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, eith... |
d63ef071ab5e984fa824ab17698dfbb028556e6e7425782bee3bdb8a74dd0b6c | Python | 8,108 | 234 | import time
import warnings
import torch
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.optim
import torch.utils.data
from config.config_reader import parse_args, create_parser
from dataloader.load_dataloader import load_dataloader
from model.unsupervised_model import Model
from loss.co... |
e7e96e1ae4b4a1c68adb0af7b4e7a10b3e2e5049b421e8d76f7ef0cb2c8a0613 | Python | 8,109 | 194 | # 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... |
9d4d7a3192173d05feed6a62686ce8dfddaa9ea8edf41bbcc74babe3eb603772 | Python | 8,113 | 205 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
709d977b7d66dc7f8476311229124bd819228ca30ec02826e72ef7f30e10e235 | Python | 8,114 | 208 | ####################################################################################################
# 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 ... |
b77b20e4c174d3d7d958c678f846e88f07cbc833ba50be6a300d9d9d798096a6 | Python | 8,120 | 233 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 27 16:37:21 2021
@author: Hiroshi Yokoyama
"""
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)
... |
1c92ff4d8fb96145e2c82b564b88f9d6be5a43a356be3872e6120d7ce7907687 | Python | 8,122 | 186 | import torch
import torch.nn as nn
import torch.nn.functional as F
import logging
from mmdet.models.registry import BACKBONES
from .fna_base_backbone import BaseBackbone
from .operations import OPS, Conv1_1, conv_dw
class MixedOp(nn.Module):
def __init__(self, C_in, C_out, stride, dilation, primitives,
... |
8267463679a8e2e6d076d8fdd5a11a855daea35e3ddf86ca5ed846d46e72d593 | Python | 8,122 | 214 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
#%%
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import connectome_tools.process_matrix as promat
import pymaid
from pymaid_creds import... |
38bf7877acc43a5c065a3e5790fc937d98ae8fcef3488995a4034e24bbe10669 | Python | 8,124 | 186 | import pandas as pd
import numpy as np
import ciso8601
import functions_basic_sak as funsak
import inspect
import os
import pathlib
import wget
import requests
import re
from tqdm import tqdm
import AIS_parameters
pd.set_option('display.max_columns', 20, 'display.width', 1500)
fname = os.path.split( ... |
7f361d5b7ef5a55059cfd6f104d9040279278348c1919bb808ac6ab23526a86f | Python | 8,125 | 205 | from collections import Counter
import os
import pickle
import subprocess
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import StratifiedKFold, GridSearchCV
from sklearn.linear_model import LogisticRegression
from sklearn.ensem... |
ac72937c52775fec8d6df80257be4b2c0dabd7e549efa8d0fa498b16348cdfa3 | Python | 8,125 | 201 | import tensorflow.keras.layers as kl
import tensorflow.keras.backend as K
import tensorflow as tf
import neurite as ne
from ddmr.utils.constants import IMG_SHAPE, DISP_MAP_SHAPE
@tf.keras.utils.register_keras_serializable()
class SpatialTransformer(kl.Layer):
"""
Adapted SpatialTransformer layer taken from V... |
ba4abfff71eeb67bfd7404a4be16c043e035b613e3999a85f9582e278f96e89e | Python | 8,129 | 226 | import os
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
from siVAE.util im... |
156844a911b3b16af44025ebf8868844caffdaeb51048bbeb6776a6ab467ad19 | Python | 8,130 | 152 | """
DyNeMo: Selecting a Run
=======================
Training DyNeMo several times on the same data can give different networks: the modes come out in a different order and, where the data do not constrain the solution well, some networks can be split or combined differently from run to run. A good default is to analys... |
14553292957010c7b8c40f19fab170e48dfe33a8e9fa503282a78fd30ac97482 | Python | 8,131 | 266 | #%%
import datetime
import time
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.cluster.hierarchy import fcluster
from scipy.cluster.hierarchy import linkage as linkage_cluster
from scipy.spatial.distance import squareform
from sklearn.me... |
14dedf01fec76f851dde8f8ab8b04106676772f38cc2fa15a9b554b54037bd75 | Python | 8,132 | 238 | # 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... |
e44cac99f52eed23d7f53169a6596158f301c2fd5218379f0f397e35ea52adad | Python | 8,133 | 228 | # 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... |
fede11f8571e6c65bc04045030a1fe08292dbc29483543bbc793958cb603c100 | Python | 8,134 | 205 | from collections import Counter
import os
import pickle
import subprocess
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import StratifiedKFold, GridSearchCV
from sklearn.linear_model import LogisticRegression
from sklearn.ensem... |
9a12ff156bfe76649863699083382567819cfd8d538cd476806de8961228b709 | Python | 8,136 | 202 | import os
import collections
from os.path import join
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
633c1b5ac21cf7a7badd2fdf54dbb5e368225c6c6caa2059b545c32f0131db35 | Python | 8,137 | 198 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
3011c6290e30a2d955cf4e7d9b795b26214576e514c60cfddb86e4e18068346a | Python | 8,139 | 204 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
17f3f25f1588c920e3191fabc27334ff8177a65c7b4c168204833ec1d48a6766 | Python | 8,140 | 195 | # 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... |
23d7b5578290260a729f270f6c739bae97340a1d340c92cebb9ad34c66cac8e9 | Python | 8,140 | 204 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
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