sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bd11269a7b8bec46fa243de34c56264a008d1451e0a73aaf7def5322e93eb7da | Python | 10,214 | 268 | import torch
import torch.nn as nn
import torch.nn.functional as F
import pickle
import random
import numpy as np
from tqdm import tqdm
from torch import Tensor
from torch.utils.data import DataLoader
from utils import *
torch.set_default_tensor_type('torch.cuda.FloatTensor')
class AutoEncoder(nn.Module)... |
b30635e9479022acfbcdb81d4d883113928a4fc99c0f234583f7addf10b3367b | Python | 10,215 | 298 | """
© Copyright 2022, Torchaudio Contributors.
Built with Sphinx using a theme provided by Read the Docs.
"""
from typing import Optional, Tuple
import torch
__all__ = ["Conformer"]
def _lengths_to_padding_mask(lengths: torch.Tensor) -> torch.Tensor:
batch_size = lengths.shape[0]
max_length = int(torch.m... |
0d0f2bb554dc66212f7efdec3988751faca63cecd0c926351efe73c709cf8a76 | Python | 10,219 | 237 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: emma
With more than one bias subgroup in each disease class, stratification is more complicated because we need to ensure that *each* bias subgroup has the same distribution of disease and subject effects (otherwise, there are distribution shift-related bias... |
fa858badfdec2ccf697fe6900bb23d26ea7f3025b21e688bb142f6a0bd73e8cf | Python | 10,220 | 338 | # coding=utf-8
# Copyright 2026 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... |
c29aa499e9d1464f8fb0839f96de859ba0f9f80dadb81d7e90e5807380a37f7c | Python | 10,221 | 263 | """
Generates a ListTomoParticle object from a input STAR file
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import numpy as np
import scipy as sp
import ... |
29c5de60158f067582d23731f2f71836c09835aa6b0ad6a8f5d865ccfa17b4fd | Python | 10,223 | 303 | import pytest
import torch
from elasticai.creator.arithmetic.fxp_converter import (
FxpParams,
)
@pytest.mark.parametrize(
"total_bits, frac_bits, signed, expected",
[
(2, 1, True, -2),
(2, 1, False, 0),
(3, 1, True, -4),
(3, 1, False, 0),
(5, 1, True, -16),
... |
f6ebb37ff21639bf170177e461cd0fbfda2d7b538f7fbae78d0918223721ea0f | Python | 10,226 | 233 | from pathlib import Path
from typing import Any, Callable, Dict, Tuple, Union
import mne
import numpy as np
from .base_dataset import BaseDataset
from ...utils import get_random_dir_path
def default_read_fn(file_path, **kwargs):
# Load EEG file
raw = mne.io.read_raw(file_path)
# Convert raw to epochs
... |
33e4da217a24d0d2e54127c2a596f512c364268b8ffaa32d1f39b98e79a19532 | Python | 10,227 | 255 | """
Read / Write files modules
"""
# Copyright (C) 2021 Blue Brain Project, EPFL
#
# 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 the License, or
# (at your option) any la... |
61d4b9f46d2f2a69d5d0fa003ef8f40c2752dfd7a4b1defba7eed9244e354cfb | Python | 10,227 | 246 | from __future__ import print_function
import argparse
import cProfile
import pstats
import random
import numpy as np
from examples.drake.generators import Pose, Conf, get_grasp_gen_fn, get_ik_gen_fn, \
get_motion_fn, get_pull_fn, get_collision_test, get_reachable_pose_gen_fn, get_open_trajectory, Trajectory
from... |
69d0e521edeb077eaf419060758e983cb73a1a69cc8b99c3e26bf1b04aa27101 | Python | 10,228 | 299 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from cellsim16popsParams_modified_spontan import multicompartment_params
import analysis_params
import plotting_helpers as phlp
import h5py
import os
from matplotlib import gridspec
from matplotlib.colors import LogNorm
import matplotlib.pyplot as plt
import numpy as np
imp... |
b3ffc0b03f9f3a08cb14cbce5eac40465e542741a3a1d46bf74491fa9c0ebdeb | Python | 10,228 | 333 | """Class for defining 3D atom environments.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
from __future__ import division, print_function
from functools import reduce
import numpy as np
import rdkit.Chem
import smart_open
from e3fp.fingerprint import array_ops
PDB_LINE = (
"HETATM{atom_id:>5d} {name:<4s} L... |
004558d2aa27cb210c82fe03a3674836baea500c149365d84aa1cceb9d2ecde9 | Python | 10,230 | 330 | """
pygments.util
~~~~~~~~~~~~~
Utility functions.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
from io import TextIOWrapper
split_path_re = re.compile(r'[/\\ ]')
doctype_lookup_re = re.compile(r'''
<!DOCTYPE\s+(
... |
c1fd29332353051bd36eaad55ac16f33343c7bdeb97625e1a1599a458e99bbb1 | Python | 10,232 | 286 | import os
import gzip
import numba
import numpy as np
import pandas as pd
from numba import njit, prange
from .smooth import _load_smoothed_chrom
from .utils import _check_data_dir, _iter_bed, _load_chrom_mat, _parse_cell_names, echo
@njit(parallel=True)
def _calc_mean_mfracs(
data_chrom,
indices_chrom,
... |
484f0c5719f9cfecd62f44c551c126cc906932d65179f9f6404f1dd214799603 | Python | 10,234 | 233 | import pandas as pd
import numpy as np
import mdtraj as md
import itertools
import os
import MDAnalysis
from MDAnalysis import transformations
def initProteins():
proteins = pd.DataFrame(columns=['pH','ionic','fasta'])
fasta_CPEB4 = """MGDYGFGVLVQSNTGNKSAFPVRFHPHLQPPHHHQNATPSPAAFINNNTAANGSSAGSAWLFP
APATHNIQDEI... |
954ce1b1847086fdfd335e393a547c19dde508c47c39986ae22fda5300b23d59 | Python | 10,234 | 263 | """
Generates a ListTomoParticle object from a input STAR file
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import numpy as np
import scipy as sp
import ... |
316b25d311b91404f6313b793bda89650b08190ce885590cb35bfaffacdf694d | Python | 10,236 | 475 | #!/usr/bin/python
# -*- coding:utf-8 -*-
# -*-mode:python ; tab-width:4 -*- ex:set tabstop=4 shiftwidth=4 expandtab: -*-
#
GAMMA_MIN = 0.1
GAMMA_MAX = 10.0
CONTRAST_MIN = -50
CONTRAST_MAX = 100
UNSIGNED_INT_MAX = 0xFFFFFFFF
UNSIGNED_LONG_LONG_MAX = 0xFFFFFFFFFFFFFFFF
# frame state code
class GxFrameSta... |
da95c9f138621fc49bde9b0d19f9a437b2a8b2ad9664f9ba83c49e779524df20 | Python | 10,237 | 298 | from __future__ import print_function
import cProfile
import math
import os
import pstats
from collections import namedtuple
from pddlstream.algorithms.focused import solve_focused
from pddlstream.language.function import FunctionInfo
from pddlstream.language.generator import from_fn, from_test
from examples.discret... |
ec7f2469f81428db278ffa9f2d54e34f22c31a3ed1b7fac3f8720e5b8369eddf | Python | 10,242 | 193 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 5 11:18:19 2021
This script compute the value, trial by trial, of the priors and the posteriors.
These variables can be computed with generative or inferred priors, with optimal or fitted parameter
The script also computes derivative from these vari... |
d444a9ab0d22ba94bf2bba6164ae73b21544e42cf2f41b462c55385ba127bdaf | Python | 10,243 | 311 | """Build Environment used for isolation during sdist building
"""
import logging
import os
import pathlib
import site
import sys
import textwrap
from collections import OrderedDict
from types import TracebackType
from typing import TYPE_CHECKING, Iterable, List, Optional, Set, Tuple, Type, Union
from pip._vendor.cert... |
92c1ab28d152e936156db40b1e1b4e1e779067d4ea9834000f8610fa46751500 | Python | 10,244 | 295 | """
Calibration slopes for right- and interval-censored survival predictions.
Author: Weijie Sun
"""
from __future__ import annotations
from collections.abc import Callable, Sequence
import numpy as np
from scipy.optimize import brentq
from SurvivalEVAL.evaluations.util import interpolated_curve
def _invert_from... |
9895f5efdf2d8d98b3f6fcbf7c8bd7be83289c2317b2aa3cc118b94ceae44638 | Python | 10,245 | 311 | #!/usr/bin/env python
# coding: utf-8
### This scripts was used for calculating the accuracy of each integration methods in predicting genes.
### Detail usages can be found in PredictGenes.ipynb
import pandas as pd
import numpy as np
from scipy import stats
import scipy.stats as st
import seaborn as sns
import matplo... |
0fde126ca92d226f4512ae35a10380baecab50f8219e16bf64c75b00838aec58 | Python | 10,247 | 295 | import unittest
import numpy as np
import numba
from neurolib.control.optimal_control.oc import (
solve_adjoint,
compute_gradient,
update_control_with_limit,
convert_interval,
limit_control_to_interval,
)
from neurolib.control.optimal_control.oc_wc import OcWc
from neurolib.models.wc import WCModel
... |
ca91cf0fdae6da52b582eff59cb0f220f94241a1b64a9e3bb644af322a660f2a | Python | 10,247 | 182 | import torch
from torch import nn
from torchdrug import core, data
from torchdrug.layers import functional
from torchdrug.core import Registry as R
# from torchdrug.data import CG22_PackedProtein
from cg_maml_steps.cg_protein import CG22_PackedProtein
# ** should be registered in torchdrug.layers.geometr... |
0b89f8a1f50aae0ac90660fa9f9ad5aa8799ad14393dfa854489f21d1887dde4 | Python | 10,249 | 262 | """
Test for reading Gaussian files, determining bond orders and
GAFF atom types. The test reads a correct SDF file with
charges and bond orders specifies, and then compares the
molecular structure to what is generated based on the
Gaussian output.
If the script is run with an addition (random) flag, more
verbose o... |
68a3203f380895b6d09dde8287e0d5e7dfc49b1f40019f577920bbefcafd47ce | Python | 10,249 | 264 | # Copyright (c) 2019 Mwiza Kunda
# Copyright (C) 2017 Sarah Parisot <s.parisot@imperial.ac.uk>, Sofia Ira Ktena <ira.ktena@imperial.ac.uk>
#
# 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, eithe... |
bd23914f4d7be760e982693eba07b635e7ab3d54e767f7ab39016d0a580d7195 | Python | 10,250 | 270 | from dreamcoder.dreamcoder import ecIterator
from dreamcoder.domains.text.makeTextTasks import makeTasks, loadPBETasks
from dreamcoder.domains.text.textPrimitives import primitives
from dreamcoder.domains.list.listPrimitives import bootstrapTarget
from dreamcoder.enumeration import *
import os
import datetime
import r... |
f91d1d059eeff8c3bf7272fec293d56d051da2d7f1487ccc79e6867e3a9bff72 | Python | 10,251 | 234 | """Region-operations mixin for the CCF boundary editor.
Carries region-level commands invoked from the region list/tree context
menus and toolbar: zoom-to-region, delete/restore a label across the whole
volume, per-region colour overrides (prompt / set / reset / refresh),
drop-unused-labels, and reset-region (thi... |
2277330c97f7413378cc6d831c2708f83218872d4b0a057b873fd09deb46e6f1 | Python | 10,252 | 297 | import re
import inspect
import warnings
import functools
from decorator import decorator
import torch
from torch import nn
from torchdrug import data
def copy_args(obj, args=None, ignore=None):
"""
Copy argument documentation from another function to fill the document of \*\*kwargs in this function.
... |
27b13e7c731d05fb500c2326a7a4884b5b210472a1fe288092311e9e29596c6a | Python | 10,255 | 259 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 22 20:52:47 2021
Notes:
- ``mne coreg`` to create -trans.fif file
- ``mne watershed_bem``to compute the requried inner_skull.surf etc. (4 min)
- ``mne make_scalp_surfaces`` also generates one of the surface file but not all (1 min)
... |
a633a88361e139f879cd0d8af5dfd6d62f99d5a2620db29c6c2e022843ef4865 | Python | 10,260 | 253 | import platform
import serial
import serial.tools.list_ports
import time
import numpy as np
import threading
from control._def import *
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
# temporary
class Microcontroller2():
def __init__(self):
self.serial = None
self... |
2c80ab41d4d351687cba20be101d4a111ea8cd092df689195e75d898be6257f5 | Python | 10,261 | 297 | import numpy as np
from scipy.stats import gamma, norm, multivariate_normal
from scipy.stats import beta as beta_rv
import sys
sys.path.append("../../lib_c/")
from smc2 import smc_c
import matplotlib.pyplot as plt
import time
from numpy.random import multivariate_normal as multi_norm
from scipy.misc import logsumexp
sy... |
aa0aac91707d8d0f5689a18722fe723b50e19cf591f23778e657d0bc3c5eee9d | Python | 10,261 | 241 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import cProfile
import os
import pstats
import sys
sys.path.append(os.environ['PDDLSTREAM_PATH'])
from examples.pybullet.utils.pybullet_tools.pr2_primitives import Conf, control_commands, Attach, Detach
from examples.pybullet.utils.pybullet... |
93ac827532f89a6da9669c9f0be697e9a69cf122642a32166a569df0fa7c765f | Python | 10,262 | 203 | """
MAIN ALGORITHM OF ANDEPED
This file contains the initialization and operation of the AnDePeD algorithm and its improvements.
"""
import numpy as np
import AnDePeD.ReRe.status_bar as bar
def initialize_rere(self):
self.values = self.data['value'].to_numpy()
# the first B-1 indices won't be used for pred... |
ddcb9c81b33570460e52270504cf683f3c9108e4f6ba98e700a6137a2b5eec42 | Python | 10,265 | 271 | r"""Test PubChem JSON format using the OpenBabel Python bindings
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pybindtest -VV
You could also "chdir" into build/te... |
13bee6af80e36032bbbdf29d1b9547acbb3ac69fbd6f2957ed600cb79da82fbf | Python | 10,267 | 172 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
1744c1363624326b5efd88356e12951d748d59634510f203520c21b87764a31f | Python | 10,270 | 248 | """distutils.extension
Provides the Extension class, used to describe C/C++ extension
modules in setup scripts."""
import os
import warnings
# This class is really only used by the "build_ext" command, so it might
# make sense to put it in distutils.command.build_ext. However, that
# module is already big enough, a... |
041916544fea9b2dbe39c23d939a93a272adb29f83829a30ca5c1dc755007279 | Python | 10,274 | 234 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import torch
import torch.nn as nn
import torch.autograd as autograd
import torch.nn.functional as F
import torch.utils
import torch.utils.checkpoint
from .utils.constants_torch import use_cuda
# inner module ====... |
e5bf684ee0a6b922cb9425082c7a3c225b52647d88662cafa6dde1dc79f1bef4 | Python | 10,275 | 256 | #!/usr/bin/env python3
"""
Refresh the JSON fixtures in test/fixtures/ from the live Wikidata/Wikimedia
Commons APIs.
The fixtures are deliberately *pruned* copies of real entities: only the
languages, claims and sitelinks actually used by the test suite are kept, so
the files stay small, readable and stable. Volatile... |
69421c405d42d8c692bda805e51fa199401f8ccb079ed22c3a97d1b06a544de3 | Python | 10,276 | 255 | from __future__ import annotations
import re
from typing import Any
from wikibaseintegrator.entities.baseentity import BaseEntity
from wikibaseintegrator.models.forms import Form, Forms
from wikibaseintegrator.models.lemmas import Lemmas
from wikibaseintegrator.models.senses import Sense, Senses
from wikibas... |
6c5465c4cb98806ac880d8de03603d6baa371d047b125a7443ee619c15950b01 | Python | 10,276 | 318 | # coding=utf-8
# Copyright 2026 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... |
b7f729a89001dff0a7f8de71dd964e9a6914489b018a535546aca46477948398 | Python | 10,278 | 158 | from enum import Enum
import numpy
import json
import re
class ComputationBackendType(str, Enum):
"""
Type of computational backend to use for the lagrangian.
"""
TENSORFLOW = 'tf'
PYTORCH = 'torch'
class IntegrationMethod(str, Enum):
"""
Type of method to get the voltage gradients.
... |
104c873ace1e21f714f265bc1a8ab01f5952738a2133df827765b1f299366c9a | Python | 10,279 | 239 | from __future__ import print_function
from copy import deepcopy
from time import time
from pddlstream.algorithms.downward import run_search, TEMP_DIR, write_pddl
from pddlstream.algorithms.instantiate_task import write_sas_task, translate_and_write_pddl
from pddlstream.utils import INF, Verbose, safe_rm_dir
# TODO:... |
e89c9be57be4b93bb872944b068d5a6ac777e7354088d4d969d4a3c247d41c00 | Python | 10,280 | 269 | # -*- coding: utf-8 -*-
"""(Keras) Layers for building Behler-Parrinello symmetry functions
This module implements the base layers `*_SF`, which computes the symmetry
functions. The layers handelling the computation of atom-centered fingerprints
and the caching of Jacobian are implemented in `networks.bpnn.BPFingerpr... |
f3957fcd0c93149f5f2fa280722821fcab51e2b928a2604cf83b320195e1faac | Python | 10,281 | 304 | import numpy as onp
from autograd.extend import JVPNode, def_linear, defjvp, defjvp_argnum, register_notrace, vspace
from ..util import func
from . import numpy_wrapper as anp
from .numpy_boxes import ArrayBox
from .numpy_vjps import (
balanced_eq,
dot_adjoint_0,
dot_adjoint_1,
match_complex,
nogr... |
45a9ea0dfc675f800e7684886cdc1756f81fe869315849783b9629175cd0866d | Python | 10,285 | 297 | try:
import binutil # required to import from dreamcoder modules
except ModuleNotFoundError:
import bin.binutil # alt import if called as module
from dreamcoder.dreamcoder import *
from dreamcoder.grammar import *
from dreamcoder.program import *
import numpy as np
from dreamcoder.type import *
tobject =... |
d287f8ad644daafd9075d1d288a9074bc3304d2405760bf17d573ca433004097 | Python | 10,286 | 280 | """
code adapted from: https://raw.githubusercontent.com/facebookresearch/FixRes/main/imnet_extract/Res.py
"""
import torch
from torch import Tensor
import torch.nn as nn
from typing import Type, Any, Callable, Union, List, Optional
__all__ = ['ResNetV2', 'resnet18V2']
def conv3x3(in_planes: int, out_planes: int,... |
f3b5e5ae415b3ea86c11c53a9999d57a6448c7c6535f961b299667852da4187f | Python | 10,287 | 175 | """NEVER.py 2026-10-09. Pre-registration: 04-NOTES/PREREG-2026-10-09b-NEVER.md
Flies that never existed. From the antennal-lobe cut-out of Shiu et al.'s v783 file (3,431 neurons, both lobes) I keep the parts
list (every neuron's type and side) and the rules (for each ordered pair of types and same/different side: the... |
12012048828c125be9b4ef7cfdbb7bfe7c87fc6eb171633c2b7e83bdda672d90 | Python | 10,288 | 263 | """
Generates Surface objects from and input STAR file or tomogram
Input: - Either a STAR file of particles and the particle average or a segmented tomogram
Output: - An output STAR file with the set of Surface objects generated which are stored in disk
"""
################# Package import
import os
... |
4d509434fca338c68e6bbe22abf9f40967f452f4f91a22003028f8e8b6a456d7 | Python | 10,288 | 195 | import pandas as pd
import numpy as np
import warnings
warnings.filterwarnings(action='ignore')
import matplotlib.pyplot as plt
import json
from sklearn.decomposition import PCA
from sklearn.pipeline import Pipeline
from xgboost import XGBClassifier
from sklearn.linear_model import Lasso
from sklearn.metrics import cl... |
e188be639f360e1636680240893c21f00783033fbaa4e1b809a5f276c2bd1bcd | Python | 10,288 | 272 | from argparse import ArgumentParser
import functools
from pathlib import Path
import sys
import subprocess
from typing import List, Optional
import numpy as np
from scipy.stats import pearsonr, spearmanr
from multiprocessing import Pool
import pandas as pd
from tqdm import tqdm
_encoding = sys.getdefaultencoding()
in... |
5fe9d6784151b324d06b65f81fe6df76880431e7518fec2ce691459ea848c193 | Python | 10,289 | 291 | """
Created on 02/06/2020
Modified on 16/06/2020
:author: Mahyar Osanlouy, Gonzalo D. Maso Talou, Chinchien Lin
:summary:
"""
import os
import SimpleITK as SITK
from src.utils import sitk_utils as sutils
from src.registration.registration_parameters import RegistrationParameters
__image_type__ = SITK.... |
8aab9570c0b98a956f113551137775ac6800798c6fe08d9a36154394c8924533 | Python | 10,289 | 275 | # __main__.py
import sys
import importlib
from fba import __version__
from fba.parsers import parse_args
from fba.utils import open_by_suffix, get_logger
def main():
args = parse_args()
logger = get_logger(logger_name=__name__)
banner = """
█████▒▄▄▄▄ ▄▄▄
▓██ ▒▓█████▄ ▒████▄
▒████ ░▒█... |
8e7e87ad34f0039f6819706c31eb33d7b95aefccd55a2051c7169d46c43d9702 | Python | 10,292 | 236 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
#
# 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://ww... |
97c7d18220ce08f218977cb7bbaa61febaf60bc96ddaf342aadf2449fef5876b | Python | 10,292 | 249 | """
Convolutional autoencoder
"""
from operator import index
import keras
import numpy as np
import pandas as pd
import time_series_tools as ts_tools
class ConvolutionalAutoencoder():
"""
"""
def __init__(
self, window_steps, model_to_load=None, encoder_model_to_load=None, decoder_model_to_load=... |
f1f63c49e1ad88a4c2953ed7c205cb13f098cdbd9d67cb52fc156adf9014e035 | Python | 10,294 | 290 | # external modules
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pyplot as plt
import os
import numpy as np
from matplotlib import cm
import pandas as pd
from scipy.signal import find_peaks, peak_widths
import seaborn as sns
import scipy.stats as stats
def format_global(value):
if (value... |
19b5b09e3cba6f13711285c713279de275f6a46aba5cfa15776fb6a790217cfa | Python | 10,299 | 215 | import warnings
from typing import Optional
import numpy as np
import torch
import torch.nn
from . import ArrayOrTensor, OptionalArrayOrTensor
from .base import BaseModel
class RP(BaseModel):
def __init__(self, n: int, nprojections: Optional[int] = None, indegree: int = 5, threshold: float = 0.1,
... |
1e8d61d8d08228f743cd2d3a9e881a46e16cf64458e615b60d851e0fbdc0be76 | Python | 10,300 | 282 | import pylink
from EyeLinkCoreGraphicsPsychoPy import EyeLinkCoreGraphicsPsychoPy
from string import ascii_letters, digits
import numpy as np
from psychopy import core
import sys
import platform
import time
import rtPupil_config
from PsychoPyFunctions import instructions_screens, terminate_task
def validate_edf_fname... |
87634da95fc8ec898c43ade5a0d651796130a3cbf99450b22825fb144f4936fe | Python | 10,303 | 261 | import os
import subprocess
import warnings
from datetime import datetime
import signal
from contextlib import contextmanager
import numpy as np
from numpy import dot, transpose, sqrt
from numpy.linalg import svd, det
import torch
import yaml
from rdkit import Chem
from rdkit.Chem import RemoveHs, MolToPDBFile
from tor... |
a055885a433951c47a9dfb29fb5cc784ab38430fef08f81ad5277eb8936beb3b | Python | 10,306 | 245 | import torch
import numpy as np
from tqdm import tqdm, trange
import tifffile
import os
from core.load import load_data
from core.models.Model import create_model
from core.utils.misc import *
from core.utils.Coord import Coord
from glbSettings import *
torch.backends.cuda.matmul.allow_tf32=True
torch.backen... |
a073a945d8902d5d50b6920a8e09522394c79b75dd1124c705ea07b7b7d4a8ca | Python | 10,306 | 349 | import random
import torch
import numpy as np
from scipy.special import softmax
import analysis_utils as au
import fit_data as fd
no_food_water = 0
food_water = 1
more_food_water = 4
# probability of transfering from s1 to p1, p2, p3
s1_food = 0.8
s1_water = 0.15
s1_more_food = 0.05
# probability of transfering fro... |
3b1043be82fb0eac82ca21bbad21882ba96d77a07290d54d1cd152c21fcb2b7b | Python | 10,307 | 299 | """
Script for computing statistics about the profile (along different penetration values) clouds
of points extracted from a network of filaments attached to a membrane
VERY IMPORTANT: all cloud of points will be compressed to a 2D Euclidean space
Input: - Path to a membrane attached filament network... |
119e7ee2cb1d93c46f426f2dc7f75e062ccb6f1d3fc6fc6bd50aac9c986c962a | Python | 10,308 | 266 | #!/usr/bin/env python
import time
import pybullet as p
import copy
from perception_tools.perception import Perception
from perception_tools.common import NAME_TEMPLATE, get_body_urdf
from plan_tools.common import get_color
from pybullet_tools.utils import create_box, ClientSaver, set_point, wait_for_user, pairwise_co... |
4f3777c4466306b098dab97e05f0423ce8759d1bacee2616257a20c76c5d61d3 | Python | 10,309 | 305 | import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.ticker import MaxNLocator
import sklearn.metrics as sk_metrics
import scipy.stats
import pandas as pd
import matplotlib.dates as mdates
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
def p... |
2119bf86330dde093ecc5c84280e82aee30029ddc00698b30f8da0c74d78c6cb | Python | 10,318 | 210 | import numpy as np
def FullfillData(m_AbsPSD, v_SessionTimes, d_stepSize):
"""
Fill missing data in the PSD matrix by extending the available data based on session times.
Parameters:
- m_AbsPSD (array-like): Matrix containing the power spectral density (PSD) data.
- v_SessionTimes (array-l... |
96ba0f29e4d19438de6c9f69ae09c21b825920c407dc0399e07ac00075022e76 | Python | 10,320 | 303 | '''
Script that runs the DNN on PLEC data
'''
import argparse
import math
import os
from collections import defaultdict
from statistics import mean
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from datasets import CustomDatasetDB,... |
df5b4c211bd4afc6e0269e29d7d1f09c935514ab6ed48506a0503d86edf2f549 | Python | 10,322 | 281 | """
Calculations that write attributes on a ``Molecule``
A calculation is a function that takes the ``Universe`` and returns one value
per atom, stored as an attribute under the calculation's name, or one that
writes a data object itself and returns None, such as hydrogen bonds. An updating
calculation runs on every f... |
6a935acbc3c8e1435fee2bd32b7f1692f096878ff2dd8ec30092bb2cfe5e0f6f | Python | 10,323 | 263 | # -*- coding: utf-8 -*-
# @title Generate parameters related to synapses
# @file Synapses.py
# @author Romain Beaubois
# @copyright
# SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief Generate parameters related to synaps... |
e7da65315ed5e9c1e04090f7a595e8a95ef207021471424dee507fef4104ec00 | Python | 10,326 | 234 | # -*- coding: utf-8 -*-
import torch
import torch.nn as nn
from supar.config import Config
from supar.model import Model
from supar.models.dep.biaffine.transform import CoNLL
from supar.modules import MLP, Biaffine
from supar.structs import DependencyCRF, MatrixTree
from supar.utils.common import MIN
class BiaffineD... |
d22ae6ddf6852de0585d3939d3f6d35ae7615aa6e9da3c299fda4a1bb827d502 | Python | 10,329 | 286 | """Slide-level training with ordmet script.
Copyright (c) 2024 University of Michigan. All rights reserved.
Licensed under the MIT License. See LICENSE for license information.
"""
import yaml
import logging
from functools import partial
from typing import Dict, Any, List
import torch
import pytorch_lightning as pl... |
40a62bd9fe865e1f56b9659fda969b02d1c6c2fa9daa593992af25cd8e9fd85f | Python | 10,330 | 284 | # ----------------------------------------------------------------------
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/... |
4b92defb56ac9b45a8227da031c41411a295bd5b13c73c2559d36aa3b4e40dff | Python | 10,330 | 218 | '''
Description:
Visualization.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import numpy as np
import tabulate
import pandas as pd
from sklearn.neighbors import NearestNeighbors
from plotting.__init__ import *
from plotting import _removeAllBorders, _removeTopRightBorders
# ==============================... |
5f4c7b548997acebbff78e5336e50183db0d6c023638146c866fdc751dffc263 | Python | 10,331 | 203 | #!/usr/bin/env python
import warnings
from typing import Tuple, Optional
import torch
from torch import Tensor
from torch.nn.modules.linear import Linear
from torch.nn.init import xavier_uniform_
from torch.nn.init import constant_
from torch.nn.init import xavier_normal_
from torch.nn.parameter import Par... |
66024b352b90d79a47a82801904960fc924200fc5c1aad8e9c7700d47e1d6e8e | Python | 10,332 | 161 | """LIU_WILSON.py 2026-10-02. Pre-registration: 04-NOTES/PREREG-2026-10-02e-LIU-WILSON.md
Two known answers from Liu & Wilson (2013, PNAS 110:10294): (A) do the connectome's synapse counts predict the six
connection rates of their paired recordings between GABAergic local neurons, glutamatergic local neurons and PNs (Fi... |
d7aef2c83c73e0b1b73d3c270cc65c57314e264f29ad049ee6bbb2018966bd86 | Python | 10,332 | 344 | """Utility functions for file and path handling."""
from __future__ import annotations
import contextlib
import os
import socket
from copy import deepcopy
from datetime import UTC, datetime
from logging import getLogger
from pathlib import Path
from random import randint
from shutil import copy, copytree, ignore_patt... |
d5e49010802265e13d8327e3a4e0b8c5d4c24b630629333a726342605981af97 | Python | 10,335 | 280 | """
Script for doing univariate point spatial analysis on stacks of actin filaments
Input: - Path to the input tomogram with filament cross-correlation map
Output: - StackPlotUni object pickled
- Figures with the analysis
"""
__author__ = 'Antonio Martinez-Sanchez'
#######################... |
78bd5a82205b79f2c29136caddb805799c8ad4432ae066b9e33342b9bce11bb0 | Python | 10,336 | 212 | import os
import sys
import time
import json
import random
import shutil
import scipy.io
import numpy as np
from os.path import exists
import matplotlib.pyplot as plt
import protocol_file as protocols_many
unique_ID = sys.argv[1]
params_file = 'params' + unique_ID + '.param'
params_v = np.genfromtxt(para... |
fd83e248f64ac55629b57d1b863b81552bfca31b65040bc46f77143574672928 | Python | 10,336 | 290 | # coding=utf-8
# Copyright 2026 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... |
8c4b404ccafa37aed70137a4972d388338fe19c44b324de54f1c42de189d08aa | Python | 10,338 | 260 | #!/usr/bin/env python3
import os
import sys
import argparse
import functools
import subprocess
import re
import shutil
import datetime
import math
import collections
import threading
import flex_ddg_db3
use_multiprocessing = False
if use_multiprocessing:
import multiprocessing
# The Reporter class is useful for... |
5bccfee3b9121be9e9349e2325475553d44bee246ad0abafad55bda88c5baba6 | Python | 10,340 | 255 | import torch
from torch import nn, optim
from torch.nn import functional as F
from scipy import optimize
from scipy.optimize import minimize
import numpy as np
from torch.nn.parameter import Parameter
from sklearn import linear_model
# from TransCal import cal_acc_error
def get_weight(source_train_feature, target_fe... |
82e321e059850626a6a9a400e0fc380733e5a6e86115da6949a70265917bb6de | Python | 10,340 | 228 | """
Utility functions that serve for creating the final tables and visualizations
of the data
@author: trianaa1
"""
import numpy as np
import pandas as pd
import netplotbrain as npb
from matplotlib.colors import LinearSegmentedColormap
def lags_to_table(data, real_corr_values, variables, network_mapping, alpha, thr... |
f989941df21ea2705d17b166404508ae00db70f14ebf3a19aa24b295260cc968 | Python | 10,341 | 245 | import os
import bct
import numpy as np
from scipy.stats import spearmanr
from utils import pickle_load, make_dir, phi_stats, \
med_avg_weight, med_euc_dist, \
mannwhitneyu_print, save_plot
from rich_feeder_peripheral import rich_feeder_peripheral
import seaborn as sns
import mat... |
6f6495964781acd0a0ec26c3a668de5498aa6c10754dd19354f3052a97a314d0 | Python | 10,342 | 297 | # -*- coding: utf-8 -*-
"""
Created on Tue Sep 24 11:40:41 2019
@author: Laure Spieser and Boris Burle
Laboratoire de Neurosciences Cognitives
UMR 7291, CNRS, Aix-Marseille Université
3, Place Victor Hugo
13331 Marseille cedex 3
This file is part of Myonset.
Myonset is free software: you can redistribute it and/or m... |
e91a711e6ae54fe0cf1b15210310e4972fcda54e87251396779a08af359f1d4e | Python | 10,344 | 296 | from rdkit import Chem
import numpy as np
from rdkit.Chem import Draw
# patts = [
# '[c][N]([C])[C]', #dimethylamino diethylamino
# '[c][N]([c])[C]', #DPA
# '[c][N]([c])[c]', #TPA
# '[c][O][C]', #methoxy
# '[c][O][c]', #DPO
# '[c][S][c][c][N][c]', #phenothiazine
# '[s]', #thiophene
# '[... |
ee6935053e44a2dc448c44a49a23a2a496adce19c569b6c65c4b22fe672a515a | Python | 10,346 | 248 | import io
import json
import os
import tempfile
import unittest
from unittest.mock import patch
from hed.scripts.hed_extract_bids_sidecar import main
class TestExtractBidsSidecar(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.data_root = os.path.realpath(
os.path.join(os.path.d... |
32c3f583e55d04adff3ef15a2b1d5775ae315e94eea3be3d15fbce61c2acb751 | Python | 10,359 | 328 | # coding=utf-8
# Copyright 2026 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... |
844e710e48f76734deca09b7728567b2b46ca66b2995464bf5635a723f195839 | Python | 10,359 | 292 | #!/usr/bin/env python3
# coding: utf-8
"""
Copyright (c) 2023-2023 Blue Brain Project/EPFL
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 requir... |
cc700be2744b1e365fa02547a45765602fa5a419b1be79d15999bba6e5ae7df2 | Python | 10,360 | 230 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import warnings
import numpy as np
from nxsdk.net.process.basicspikegen import BasicSpikeGen
from loihi_tools.compartment_tools import create_distributed_group_over_cores, create_compartment_prototype
from loihi_tools.spikegenerators import create_spikegen
from loihi_tool... |
fcf65ddb57e77f647b5ae1dc9d660d316380125505ab5db26a2bdf89c7f30982 | Python | 10,361 | 309 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# 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 ... |
8dbe678557adc5df78e2112fb68419e9b89a2fefe829e392a7f786854be18136 | Python | 10,367 | 239 | # coding=utf-8
# Copyright 2026 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... |
262f98a247e48677deff1326af82128d9074ed3257820042398a186be1c302bf | Python | 10,368 | 311 | import sys
from itertools import chain
from typing import TYPE_CHECKING, Iterable, Optional
if sys.version_info >= (3, 8):
from typing import Literal
else:
from pip._vendor.typing_extensions import Literal # pragma: no cover
from .constrain import Constrain
from .jupyter import JupyterMixin
from .measure imp... |
98e426ae44a6afebbc834092aeda2a469399975bd17a3a2d76a369a0d4088321 | Python | 10,369 | 255 | """
Functions to convert a VOX_coords_mother.txt file into a voxel_coordinates.json file.
Adds grid_group and grid_loc fields.
Run:
python vox_mother_converter.py <subject> <out_file>
to create a voxel_coordinates.json file
"""
import re
import pandas as pd
import os
from collections import defaultdict
from .conf... |
84a42ee284c01c723283fa7f2e6cd6093171b18d1d9df82741177bfcb3109b58 | Python | 10,370 | 254 | import numpy as np
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, TensorDataset
from .scoring import regression_scores, binary_classification_scores
def arch(input_dim = 200, output_dim = 1, hidden_width = 300, hidden_depth = 10):
"""
Returns a tuple of integers specifying the ar... |
984f2979f16d339bcb49f03449721c6dfcaf0c01fea4b1ac09a28495c73d642a | Python | 10,371 | 261 | # coding=utf-8
# Copyright 2026 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... |
0e5d607fb106d17866a638ff2b8c942862d559ca4342d9662bc5edd5674a4883 | Python | 10,375 | 353 | """This module contains sampler class which generates a sequence of nodes from
a network using a random walk.
All samplers should be the subclass of NodeSampler class.
"""
from abc import ABCMeta, abstractmethod
from numba import njit
import numpy as np
class NodeSampler(metaclass=ABCMeta):
"""Super class for nod... |
c7097618cac9838a627742ba32a839c74449a8c6e6b36a24d9c9e8b94d5b7a18 | Python | 10,378 | 272 | import os
import re
import sys
import zipfile
import configparser
# NSD pycortex database (Google Drive)
PYCORTEX_DB_GDRIVE_URL = (
"https://drive.google.com/file/d/1oMoOGjlrOpkphKPCC4XqUPaT0nu59kPC/view?usp=drive_link"
)
PYCORTEX_DB_ZIP_NAME = "pycortex_db_NSD.zip"
_GDRIVE_FILE_ID = re.compile(r"/file/d/([a-zA-... |
c45761332699bf41a45b18b1def3f09f71d98fb5e3bab1fdfd1669264090a894 | Python | 10,379 | 302 | # coding=utf-8
# Copyright 2026 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... |
da7634f8c0eeb5f7590653065abb2d90a768b3a5bceae3e79a0d38a26f5b5362 | Python | 10,382 | 224 | #!/usr/bin/env python
"""
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Fr... |
a48a9849aa5e0c401a688dd38a585a79be32dacb7b7103ba172deafedf0bf4fa | Python | 10,387 | 234 | """"Define the dataclass and processing of receiver data."""
from dataclasses import asdict, dataclass, field
from multiprocessing.shared_memory import SharedMemory
import numpy as np
from scipy import signal
from console.interfaces.acquisition_parameter import DDCMethod
from console.utilities import ddc
@dataclass... |
ce34c6eb71d06fc7da724ee9307f1adddaaaa3d115fe19c59d214b345c1c9e74 | Python | 10,387 | 237 | import sklearn.preprocessing
from sklearn.metrics import roc_auc_score,roc_curve,auc
import matplotlib.pyplot as plt
from torch import nn, softmax
from sklearn.metrics import roc_auc_score,roc_curve
from models import MAMFGCN
import torch.nn.functional as F
from PAE import PAE
from opt import *
from utils.metrics impor... |
9184f3acefe51ab67bfe7ad7ee0434ff078d57532a3219f5e37453798e9d9f63 | Python | 10,391 | 234 | from typing import Dict, Tuple, Union
from scipy.interpolate import griddata
import numpy as np
from ..base_transform import EEGTransform
class To2d(EEGTransform):
r'''
Taking the electrode index as the row index and the temporal index as the column index, a two-dimensional EEG signal representation with t... |
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