sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6945202150491db4df064cb0fa9714e872164ab63ac197af0437bb243eb0a858 | Python | 11,895 | 255 | import sys
## Usage: $ python scale_coef_duplex.py [2,1,1,1,1,1,1] [3,1,1,1,1,1,1] cbl_dimer.ninfo input_Y4J.bpl cbl_dimer.pdb
def usage():
print("Usage:")
print("python scale_coef_duplex_ninfo.py scale_duplex scale_nonduplex ninfo_file basepair_file cg_pdbfile\n")
print(" scale_duplex given as [x... |
01972790e38e173e4bc01c19914927c45c2b043ad171a914550de0f9a3095f7b | Python | 11,896 | 370 | import colorsys
import math
import random
import re
import numpy as np
import numpy.typing as npt
def clamp(value, min_value, max_value):
return max(min_value, min(value, max_value))
class Lab:
Kn = 18
Xn = 0.950470
Yn = 1
Zn = 1.088830
T0 = 0.137931034
T1 = 0.206896552
T2 = 0.128418... |
4f855d43f904e380ef54e8364158e6d671fcdc4073b528eaba123ac18fb3d298 | Python | 11,897 | 320 | import numpy as np
import pytest
from SurvivalEVAL import SingleTimeEvaluator, SurvivalEvaluator
from SurvivalEVAL.evaluations.discrimination import auc
@pytest.fixture
def auc_data() -> dict[str, np.ndarray]:
return {
"predict_probs": np.array([0.8, 0.3, 0.1, 0.6, 0.2, 0.01]),
"event_times": np.... |
7ce230b8de5195bcbfcadd48d4eb39eb53d21210e84b5f9e615cb49b4916ac05 | Python | 11,897 | 274 | import os
import time
from configparser import ConfigParser
import numpy as np
import torch
from e3nn.o3 import Irreps
from .utils import orbital_analysis, refine_post_node
class BaseConfig:
def __init__(self, config_file=None):
self._config = ConfigParser(inline_comment_prefixes=(';',))
... |
1cef658ec8e499d191199d3a882bd127d0e770e7c09cc2fdeaad801415adb0ba | Python | 11,899 | 295 | """Testing of sequence unrolling function."""
import tempfile
from pathlib import Path
import numpy as np
import pypulseq as pp
import pytest
from console.interfaces.acquisition_parameter import AcquisitionParameter
from console.interfaces.dimensions import Dimensions
from console.interfaces.rx_data import RxData
fro... |
3126a4a27f56ef989db0ecb898a64b4e6d110a82e974745c578f8f6a40c03dfa | Python | 11,899 | 323 | import random
import logging
from functools import partial
from typing import List, Tuple, Dict, Optional, Any
import math
import numpy as np
import torch
from torch.nn import ModuleList
import torchvision
from torchvision.transforms import Compose, RandomApply
from torchvision.transforms import functional as F
fro... |
b81f9c07edd0e1b9970cb2e96ce5a4985be2c3e15d7b7f73c8c57ab4a2765874 | Python | 11,903 | 289 | import logging
from datetime import datetime
from logging import Handler, LogRecord
from pathlib import Path
from types import ModuleType
from typing import ClassVar, Iterable, List, Optional, Type, Union
from pip._vendor.rich._null_file import NullFile
from . import get_console
from ._log_render import FormatTimeCal... |
caed1b1d44c99d09616773299a6aabed5e99c3df57f51186cca3b3cda1ee2ad0 | Python | 11,907 | 224 | import pathlib
import sys
import argparse
from datetime import datetime, timedelta, time
import numpy as np
import pause
import logging
import cv2
from logging.handlers import RotatingFileHandler
from modules.data_collection import DataCollector
from modules.object_detection import DetectorBase
from modules.upload_aut... |
aba934739028876984f099e57d394267c2c37cd3a0f6767b506b88672ce6e61c | Python | 11,908 | 291 | #!/usr/bin/python
# -*- coding:utf-8 -*-
# -*-mode:python ; tab-width:4 -*- ex:set tabstop=4 shiftwidth=4 expandtab: -*-
#
from ctypes import *
import sys
if sys.platform == 'linux2' or sys.platform == 'linux':
try:
dll = CDLL('/usr/lib/libgxiapi.so')
except OSError:
print('Cannot ... |
edf000ca69c920494faed56070cf29ba3fa42f9172f5aead58cc25caa397636e | Python | 11,909 | 258 | import lavaset.best_cut_node as best_cut_node
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
class StochasticBosque:
def __init__(self, minparent=2, minleaf=1, nvartosample=None, ntrees=100, nsamtosample=None, method='g', oobe=False, weights=None):
self.minparent = minparen... |
cfa823604ced12bc4b01f7f522fb144dc91b54cd4ff3bcfa91af3d8359194051 | Python | 11,910 | 332 | import warnings
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
import pytest
from scipy.stats import chi2
from SurvivalEVAL import (
CompetingRisksEvaluator,
SingleTimeEvaluator,
SurvivalEvaluator,
one_calibration,
one_calibration_cr,
)
def _weighted... |
aac51cb0044a6eba18301f4e65d7faa95d51086d276a953e6e1d02036e0a5e83 | Python | 11,912 | 274 | # 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... |
2c6c4c3659e6a8b850b314e8ea5357bc8b3b1b6f2d4257f1d789ef21c2dedcd9 | Python | 11,918 | 294 | """Slice-thumbnail filmstrip mixin for the CCF Boundary Editor.
A horizontal strip of small thumbnails sits beneath the canvas: the
current slice in the centre, plus ``RADIUS`` neighbours on either side
(``FILMSTRIP_COUNT = 2 * RADIUS + 1`` thumbnails total). Each thumbnail
shows the modified slice for that index... |
f251b79822856cf0a9f54540f70bb56619b0af5cec8e18a21ff92bbefbda454c | Python | 11,918 | 318 |
import numpy as np
import tensorflow as tf
slim = tf.contrib.slim
_BATCH_NORM_DECAY = 0.9
_BATCH_NORM_EPSILON = 1e-05
_LEAKY_RELU = 0.1
_ANCHORS = [(12, 16), (19, 36), (40, 28),
(36, 75), (76, 55), (72, 146),
(142, 110), (192, 243), (459, 401)]
@tf.contrib.framework.add_arg_scope
def _fixed_... |
eb5189c73422a742089e1b8eebd648e466cd43cd97103501ff51a0e7f2ad5287 | Python | 11,920 | 330 | import json
import os
import sys
import tempfile
from contextlib import contextmanager
from os.path import abspath
from os.path import join as pjoin
from subprocess import STDOUT, check_call, check_output
from ._in_process import _in_proc_script_path
def write_json(obj, path, **kwargs):
with open(path, 'w', enco... |
a2bbe520fd096b1901ddb8d89ee8476f9b379bb72d99a7f7145b8eb0e4ebbf39 | Python | 11,923 | 418 | auto_scale_lr = dict(base_batch_size=10, enable=False)
backend_args = None
data_root = 'F:/action_test/Corrected/'
dataset_type = 'CocoDataset'
default_hooks = dict(
checkpoint=dict(interval=1, type='CheckpointHook'),
logger=dict(interval=50, type='LoggerHook'),
param_scheduler=dict(type='ParamSchedu... |
841bfe39285bfee2af2e3a3f136baab502c424d0415d316096f7fa9b36d437ca | Python | 11,924 | 356 | """distutils.cygwinccompiler
Provides the CygwinCCompiler class, a subclass of UnixCCompiler that
handles the Cygwin port of the GNU C compiler to Windows. It also contains
the Mingw32CCompiler class which handles the mingw32 port of GCC (same as
cygwin in no-cygwin mode).
"""
import os
import re
import sys
import c... |
32554980aa1e000ac982dd6a3ee677c7651dd570958567ed5ec4e657169ccd84 | Python | 11,935 | 374 | # STAGE-1: Read, Preprocess & Save The Data
# Imports
import time
import copy
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.preprocessing import OneHotEncoder
from sklearn.model_selection import train_test_split
#print('Completed importing necessary libraries and utilities.')
# Start Timer... |
e8afc64486a9d7348372803ad5829aaacbed9cf19d6a5ec7d5fe5487215e234e | Python | 11,935 | 412 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
72a86bcce78d62a4965b11d7cabb7a9ef8b9f1f645be22fd22c4317c7e4b2489 | Python | 11,936 | 391 | import os.path as osp
from pathlib import Path
import numpy as np
import torch
import torch.utils.data as data
import cv2
import argparse
from .io import _numpy_to_tensor, _load_cpu
from .params import *
import random
from PIL import Image, ImageEnhance
import types
import torch.nn.functional as F
def img_loader(path... |
992802e8e3d7c20e1f044ee2388f06f3d646d6d696df76f0327850f0d7b092e0 | Python | 11,939 | 324 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2022/10/14 10:53
# @Author : piaoyang cao
# @File : prepare_mol_data.py
import os
import pandas as pd
import numpy
import numpy as np
import torch
import random
from molecule_fragment import *
# 处理每一个mol 形成大图
import networkx as nx
import iterto... |
243a4c2739e0b4e31a9d8e3cf47aa8c2cd40ea51802d2cf7d8f3bf6b1fc6106b | Python | 11,940 | 350 | import os
import collections
from classification_models_3D import get_submodules_from_kwargs
from ._common_blocks import GroupConv3D
from ..weights import load_model_weights
backend = None
layers = None
models = None
keras_utils = None
ModelParams = collections.namedtuple(
'ModelParams',
['model_name', 'repe... |
9b9d11e119cad705ca922250cfa9bd11e8777563af343634490be70e48e41977 | Python | 11,940 | 291 | import os
import sys
import datetime
import SimpleITK as sitk
import numpy as np
from shutil import copyfile
from PIL import Image
from functools import cmp_to_key
from src.utils import file_utils as futils
from src.utils import evaluation_utils as eutils
from src.utils import sitk_utils as sutils
from... |
bd9a42c6248f584667daeac33a15abfcd244733a09e328f3a3449e675aace1fe | Python | 11,945 | 335 | import numpy
from matplotlib import pyplot as plt
"""
Various plots used in the notebooks.
"""
def plot_simplex_divergences(divergences):
"""
Fig. 2B
"""
fig = plt.figure(figsize=(7, 2.5))
ax = fig.add_subplot(1, 2, 1)
for dim, vals in divergences.items():
if dim > 0:
ax.... |
06c0ee56526aa4e4356843218dad82429dbb3a031acf22edc859ecaf954802e2 | Python | 11,947 | 404 | """
Configuration settings for simulation: logger formatting, solver configuration, other flags
"""
import logging
from logging import config as logging_config
from dataclasses import dataclass, field
from enum import Enum
from typing import Any, Dict, Optional, Tuple, NamedTuple
from termcolor import colored
import ... |
19b1ad3b40bf7b3e62d7dd51b2490349d3ff3e6433c5153e8050bef3680f7527 | Python | 11,948 | 404 | """Core recipes for VASP."""
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING, Literal
from warnings import warn
import numpy as np
from monty.os.path import zpath
from pymatgen.io.vasp import Vasprun
from quacc import flow, job
from quacc.recipes.vasp._base import (
... |
690c301aecc2a5a9fa9ad99297190aa5ccee5ccebd0ed67ded47870b1af45fee | Python | 11,949 | 241 | import os
import mne
import logging
import numpy as np
import itertools
from typing import Any, Callable, Dict, Tuple, Union
import pandas as pd
from ..module.base_dataset import BaseDataset
from ...utils import LazyLoader
_MOABBDataset = LazyLoader(
'moabb.datasets.base', install_hint='Install with `pip install... |
2e30470a90e7f5ff25ced73d31ff15915ebfce931cc69eb969f72c36d57b7063 | Python | 11,963 | 332 | # 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... |
f3fd52b6aff0853db6b3f82b6f803aa1021346b0bdcd7d59eb233c5c2796b043 | Python | 11,963 | 227 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
# Copyright 2017 The Chiron Authors. All Rights Reserved.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Created on... |
b826d048a786f78cbc024c792d5e71cbac8280c9f6a1178bf7df5eb0c2976ef3 | Python | 11,964 | 335 | # 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... |
b09749e7cc1005e4d15676c5b5657ec09c439a2b3ff632bf18358983c18efb90 | Python | 11,966 | 347 | """
Performs Univariate 2nd order analysis from a STAR file with a set of ListTomoParticles entries
Input: - A STAR file with a set of ListTomoParticles pickles
Output: - Plots with the analysis
- Matrix with the analysis for further post-processing
"""
################# Package import
im... |
bf3fa68b93bf0209cf8c270d6fa358c285ec5245925d1acce9480820ef70e74f | Python | 11,970 | 275 | #!/usr/bin/env python3.9
# compile / train a model and save the best models and the last models
import time
import locale
import pandas as pd
import numpy as np
import tensorflow as tf
from contextlib import redirect_stdout
# function to save the actual best mean loss (train and validation data) and mean accuracy mode... |
72ce99de1b43e5a9192f256dd032e4320e490d078721cb425caa6b3dd1356d27 | Python | 11,971 | 399 | # 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... |
639ad8dd20d0eb27fa8cf3ec56215d9c35d0e383ca3e5fd898fae87bfe3ecd7a | Python | 11,972 | 259 | # 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... |
14961be5728297e666071d19230038599b7c19edf08e7007b766f8f8fa44c195 | Python | 11,976 | 290 |
# -*- coding: utf-8 -*-
"""
Created on Jun 23 2023
@author: Jonas A. Thiele
"""
### Apply models build in main sample (610 subjects of HCP) to
### predict intelligence scores in the lockbox sample (196 subjects of HCP)
### for models that were trained with different numbers of the most relevant links (dete... |
29a70c62aa82bab8245765f58b4e1ed271d20a73694e60b1095bfc73579a1fcc | Python | 11,976 | 344 | """Data handling utilities involving dataframes."""
import warnings
import numpy as np
import pandas as pd
from hed.errors.exceptions import HedFileError
def add_columns(df, column_list, value="n/a"):
"""Add specified columns to df if not there.
Parameters:
df (DataFrame): Pandas dataframe.
... |
a2947426c72a2367b4001cbe0053237b963cd2d8afac248d40a8429b76612f03 | Python | 11,978 | 292 | # Node-group asset "Style Ball and Stick" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_C... |
d37f92b5122693d795b66ea8804b2ba6ce759ef65f14b6edd4ce40af0e57dbf6 | Python | 11,979 | 415 | from functools import reduce
from itertools import count
from typing import ClassVar
from .tracer import Box, Node, getval, isbox, primitive, toposort, trace
from .util import func, subval
# -------------------- reverse mode --------------------
def make_vjp(fun, x):
start_node = VJPNode.new_root()
end_valu... |
1216ed27b3c266efb3a256bec4363aa616afe50ba80cf83f1497cbeacd1cae85 | Python | 11,986 | 317 | """
This module, 'bands.py', contains recipes for performing bands and fermi surface calculations using the
bands.x and fs.x binaries from Quantum ESPRESSO via the quacc library.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.dft.kpoints import bandpath
from pymatgen.io.ase import A... |
527c650f451690b59c3b1cb78faa087f410229d6489a24834e4d79f42575fc7c | Python | 11,993 | 253 | import torch
from torch import nn
from torch.nn import functional as F
from torch.utils import data as torch_data
from torchdrug import core, tasks
from torchdrug.layers import functional
from torchdrug.core import Registry as R
@R.register("tasks.KnowledgeGraphCompletion")
class KnowledgeGraphCompletion(tasks.Task,... |
81e9bde0283e83f7cc623b2e8fb4eedb5dd8d36590371d5be6ae372dc567e87f | Python | 11,995 | 314 | """A Q-Chem calculator built on Pymatgen and Custodian functionality."""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.calculator import FileIOCalculator
from quacc.calculators.qchem.io import read_qchem, write_qchem
from quacc.calculators.qchem.params import cleanup_attrs... |
3e3e762d130ef5f2d65541c780f328640d8340dcfca136cd470cca019bcde5ef | Python | 11,998 | 195 | # 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... |
65c755146e2603de48c19b1f9823b3d2af0934bd172eded05415e23ab795fc66 | Python | 12,001 | 292 | import os
import re
import numpy as np
from scipy.sparse import coo_matrix
from .structure import Structure
from .constants import AOFT_QGRID_DEN
from .utils import atom_number2name
from .orbutils import parse_siesta_ion, parse_deeph_orbtyps, parse_gpaw_basis, read_upf, grid_R2G, GridFunc, LinearRGD
def argsort(seq):... |
8249f6781adcb07aa0ffa318cf660e2f33264b3b117b75e0aab6e5133aab3ecc | Python | 12,001 | 286 | #!/usr/bin/env python3
__author__ = "Zoe Wefers"
__credits__ = ["Ryan Huang"]
__version__ = "1.0.0"
__maintainer__ = "Zoe Wefers"
__email__ = "zoe.wefers@mail.mcgill.ca"
"""Purpose: Executable file to collect localization statistics froms users result files and skeletons/prints."""
import localization_analysis as la... |
c69851b6bb8e4815a12b74abea47fadc90428a3b22127234ca1d56517ee328b1 | Python | 12,002 | 322 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Adversarial training to unlearn bias label from disease classification
-> Adapted from Raissa/Vedant's code for unlearning scanner from Parkinson's disease prediction,
based on "Deep learning-based unlearning of dataset bias for MRI harmonisation and confound removal"... |
6db58b0148e31331e03e49018a9e34d4bf0fa26cc7b987f8fbd48c35a7a318b2 | Python | 12,003 | 194 | # 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... |
d612c4367643cde76b6cf6edc461b4acedecd289d0a28a4046f40a685e92d013 | Python | 12,007 | 232 | # This is a stand alone script that plots ECGs from body surface potentials
# simulated from monodomain simulations.
# The normalisation strategy is the same as in ecg_functions.py.
import numpy as np
from scipy import signal
import matplotlib
matplotlib.use('tkagg')
from matplotlib import pyplot as plt
# Helper functi... |
684e838f9bb77d942ebe68b27e73929273c21bb9dab43242cbec2063ffcb761e | Python | 12,012 | 307 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
"""
DETR Transformer class.
Copy-paste from torch.nn.Transformer with modifications:
* positional encodings are passed in MHattention
* extra LN at the end of encoder is removed
* decoder returns a stack of activations from all decoding... |
1f5116bcf3a50bf76b01e97431826ba94dc336ee0c8f71dd0752e6059964dec0 | Python | 12,013 | 265 | """Manager of events of temporal extent."""
import bisect
import pandas as pd
from hed.errors.exceptions import HedFileError
from hed.models import df_util, string_util
from hed.models.hed_string import HedString
from hed.models.model_constants import DefTagNames, TopTagReturnType
from hed.tools.analysis.hed_type_de... |
689e5aab097dbb764810b650f3ba838d23610909dbf69b9e90359d1eab7782ca | Python | 12,016 | 313 | # Copyright (c) 2023 Se42 Authors. 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
#
# https://www.gnu.org/licenses/why-not-lgpl.html
#
# Unless required by applicabl... |
97ebaf925435718b41287a2b82e085a5e9afc9c3430486ee339859b2b949cb08 | Python | 12,017 | 413 | import os
import sys
import time
from contextlib import contextmanager
import nibabel as nib
import nrrd
import numpy as np
import scipy
from skimage.filters import threshold_triangle as triangle
from skimage.filters import unsharp_mask
from sklearn.preprocessing import quantile_transform
sys.path.insert(
0, "/ho... |
7db18445e4e8d4b389a20ee6c31e31bd149ebab87f65bf2601041546b7a2a742 | Python | 12,019 | 272 | import torch
import numpy as np
import os
from model.TwoResNet.model import TwoResNet
from lib.utils import masked_MAE, masked_RMSE, masked_MAPE
import pytorch_lightning as pl
from model.RNN.model import Teacher
from model import const
class Cluster:
def __init__(self, label):
self.label = label
... |
9f2e122eb6e8ef553b6e9f89f3675b4e171603b788b4a2423a162578c12c26dc | Python | 12,021 | 308 | """ Logic to apply transform generated by 'bifrost register' to an image
Execute using the 'bifrost' executable installed by setuptools
"""
import logging
import os
import sys
import tempfile
import ants
import h5py
import numpy as np
import tensorflow as tf
import voxelmorph as vxm
from skimage.exposure import equ... |
a4cb35045ab3625b6325b7f86c2e8eeb1ffd76f6f375ea21ec7b002c4ea19275 | Python | 12,021 | 292 | from typing import Tuple
import numpy as np
import torch
from einops import rearrange
from einops.layers.torch import Rearrange
from torch import nn
def _pair(t):
return t if isinstance(t, tuple) else (t, t)
def _get_emb(sin_inp):
emb = torch.stack((sin_inp.sin(), sin_inp.cos()), dim=-1)
return torch.f... |
13a06d87b6985bd17d4efb305b76f17d36caf3e65501dd2fdb55b2b5a2389355 | Python | 12,026 | 185 | import argparse
import sys
from NDATools import exit_error
from NDATools.Configuration import *
from NDATools.Download import Download
logger = logging.getLogger(__name__)
def parse_args():
parser = argparse.ArgumentParser(
description='This application allows you to download files from an NDA package. ... |
558db7d1c55e3b33fbe2ef7307b1d7783410ccd92b3655939f8ce708f281632c | Python | 12,028 | 206 | """SURVIVE.py 2026-10-02. Pre-registration: 04-NOTES/PREREG-2026-10-02n-SURVIVE.md
Four checks asked for by an attack on draft 10. P1: Shiu et al.'s own Brian2 code on all 50 odour channels, published signs
and laboratory prior. P2: the census's cells re-checked in spikes. P3: the margin moved by scaling excitatory loc... |
562b3e924989dc6d1113f20c1a7e9bee896c1c584df4880b8e593dacc3a8d17f | Python | 12,029 | 370 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
019e75f423fdbeedb2916f7f75e635d6bad1c30dc97e3eb2919add5641f0a596 | Python | 12,039 | 297 | import math
import torch
from torch import nn
import time
from warnings import warn
from collections import OrderedDict
import numpy as np
class RNN_Net(nn.Module):
def __init__(self, dim_in, dim_hid, dim_out,
n_layers=2, nonlin=torch.nn.Tanh(),
bias=False, out_scale="small", g=... |
5ad13ec68c0ba8b2a52490ca3accaa58da31887cf7577daa365fea3318ff85ea | Python | 12,039 | 297 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import os
import glob
import shutil
import unittest
import subprocess
import numpy as np
from cbig.He2019.config import config
from cbig.He2019.CBIG_prepare... |
6798f39e3a86427cbcce2f4b6ecd765ab5309e9aabba64f5836504191feb9d35 | Python | 12,042 | 241 | import os, sys, argparse, time
import json
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch_geometric.data import DataLoader
#from tensorboardX import SummaryWriter
sys.path.append('..')
from models.ddi_predictor import DDIPredicto... |
fcda3e99fde3aa8c92289081fc296330fbba7a124b0c31e51c3bffaa59d0546b | Python | 12,046 | 316 | from abc import ABCMeta
from contextlib import contextmanager
from enum import StrEnum
from typing import TYPE_CHECKING, Iterator, List, NamedTuple, cast
import bpy
from bpy.types import GeometryNodeTree, NodesModifier
from databpy import (
BlenderObject,
)
from nodebpy import geometry as g
from nodebpy.builder imp... |
a5e49aecacf769f0d69f93a0dc4af57cbc6fed579651da7169131ee77333f159 | Python | 12,051 | 321 | import hashlib
import importlib.resources
import inspect
import json
from collections.abc import Callable, Hashable, Iterable, Iterator, Mapping, Sequence
from contextlib import ExitStack
from functools import wraps
from importlib.resources import Anchor
from os import environ
from pathlib import Path
from typing impor... |
0195be62a97f5e2de0ab3263b73c0ae74a2e7935213f666f6485d84601fcde64 | Python | 12,055 | 264 | """Drag-tool behaviour (sketch / paint / align) for the viewer,
packaged as a mixin so the per-mode handlers live in their own
file. Mode-switching itself (``_set_tool_mode``) is also here
since it's where all three modes coordinate.
The mixin assumes the consuming class declares these instance
attributes in its... |
40d836f020ac33458a176ba6b6fdf1e9d49a05d912c553e26937ad8407ba1a23 | Python | 12,056 | 311 | import numpy as np
from scipy.sparse.linalg import spsolve
from scipy.sparse import coo_array
from numpy.linalg import norm
import copy
from ednm.aot_residual import residual
from ednm.aot_jacobian import jacobian
def alpha_c_phi(model, dt, alpha, c, phi, ss_, t, t_AP, stimulus_protocol, verbose=True):
"""
Upd... |
b4354bc9e9b13637ea9ff64061f3c2a9ccdef7d6c03335c7ba9e61a42dfa6009 | Python | 12,056 | 304 | """
Script for extracting an analyzing a GraphMCF with a segmented membrane
(v3) 18.11.15 - Modification for not to compute filaments
Input: - Density map tomogram
- Segmentation tomogram
Output: - Connectors clusters
"""
__author__ = 'Antonio Martinez-Sanchez'
# ################ Pack... |
28144d2e52887d6cce824f295e4e7d66c00438b23c026987c50facc862daaa88 | Python | 12,059 | 245 | import numpy as np
import glob
import pickle
import random
import pandas as pd
import os
from os import path
import copy
import h5py
from collections import Counter
from itertools import groupby
from operator import itemgetter
def norm(A, B):
return (((A[0] - B[0])**2 + (A[1] - B[1])**2)**(1 / 2))
def V_unit(A0... |
a2fd985ff28bc754c404691fca62a19df32bf58e33e761733b5c060cce7a336a | Python | 12,060 | 353 | # 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... |
c433f643f424d73f6296752fdc0241de812e2a1360553ac1df1f7cb6128b0795 | Python | 12,062 | 326 | import copy
import numpy as np
import analysis_utils as au
def fit_data(df,
config_columns,
mean_columns,
metric_column,
method_column,
plot_column,
raw_data,
process_plot_column_fn_in_raw_data=lambda plot: plot,
... |
303276edc32fba4f3fc212dd24a32bebe4444992797d4efc1522c0760b8b9433 | Python | 12,065 | 279 | #!/home/dingml/anaconda3/envs/expressBert39/bin/python3
import ast
from tqdm import tqdm
import argparse
import os
import sys
import numpy as np
import pandas as pd
import torch
from torch import Tensor
import torch.nn as nn
import torch.nn.functional as F
from sklearn.model_selection import train_test_split
from torch... |
77c04b3550f1d8870b5307a718c8849639c413c1b7054d3164fc0fc479cca14d | Python | 12,068 | 400 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import torch
import torch.utils.data
import torch.nn as nn
import torch.nn.init as init
class CBIG_dataset(torch.utils.data.Dataset):
"""PyTorch datase... |
b94cf3ea842dc9b19240b5991bb74ffa7b9d2a9d71f23043d57290db5b0203cc | Python | 12,068 | 247 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat May 6 10:09:47 2023
@author: daltonm
"""
from pynwb import NWBHDF5IO
import ndx_pose
import numpy as np
import matplotlib.pyplot as plt
from importlib import sys
import neo
import elephant
from quantities import s
from scipy.stats import median_test
i... |
b86d2c3fb96a9135ef7e0de1b3c9f484728c2ca2eb6bf205c65e573284d4e80c | Python | 12,069 | 370 | """Implementation of CLI render command."""
import numpy as np
from treem import Morph, SWC
from treem.utils.geom import rotation
# pylint: disable=wildcard-import
# pylint: disable=unused-wildcard-import
# pylint: disable=redefined-builtin
from OpenGL.GL import *
from OpenGL.GLU import *
from OpenGL.GLUT import *
... |
8db2bd472b1843b599c26d6dbb86328de63ea77a3fc75e8d1720572cc21cf3f6 | Python | 12,073 | 301 | import argparse
import os
import numpy
import torch
import sys
import numpy as np
sys.path.append('.')
from src import config
from src.common import get_tensor_from_camera
def associate(first_list, second_list, offset=0.0, max_difference=0.02):
"""
Associate two dictionaries of (stamp,data). As the time stamps... |
7b73ecc24b9ff6a716ebc7ef66ec7e86b51029166b84d5c29c17a9e730cc5f92 | Python | 12,074 | 308 | #!/usr/bin/env python
# Copyright (c) 2018-2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provide BasicScenario, the basic class of all the scenarios.
"""
from __future__ import print_function
import opera... |
30be2000f315a8fa58d729764caa59d8b6e69d3caf3a15d4f5b122003ed2af4e | Python | 12,075 | 256 | #!/usr/bin/env python
# Copyright (c) 2019 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Wrapper for autonomous agents required for tracking and checking of used sensors
"""
from __future__ import print_function
import mat... |
02152b80d330bc7b5311506108d8241633f74cf2457f37a01382298d130b6bb4 | Python | 12,081 | 271 | """DeepSlice tilt in the core 2D pipeline.
The old path (`_resolve_ccf_index`) filled only the CCF index from DeepSlice and
registered to a FLAT coronal slice, discarding the predicted cut tilt. These tests
pin the new behaviour: `_resolve_ccf_plane` also returns the tilt (angle_dv->pitch,
angle_ml->yaw), `_obliq... |
2e50a54d287b78bf848f2addae868526c31ac8e44b41dd5eb352936b850fc30f | Python | 12,081 | 272 | import os
from typing import Any, Callable, Dict, List, Tuple, Union
import numpy as np
import wfdb
from scipy import signal
from wfdb.processing import resample_multichan
from ....utils import get_random_dir_path
from ..base_dataset import BaseDataset
class P2018Dataset(BaseDataset):
r'''
The PhysioNet/Com... |
551c9d2e3f212cc4f7b37a3b256e9a243e693045bd53b787f20afa00b69454a3 | Python | 12,081 | 275 | from __future__ import print_function
import time
from itertools import product, islice
from random import choice
import numpy as np
from dimensions.common import BOWLS, CUPS
from learn_tools.active_gp import STRADDLE_ACTIVE_GP, VAR_ACTIVE_GP, BATCH_MAXVAR_GP, BATCH_STRADDLE_GP
from learn_tools.active_rf import BATC... |
f0497111eec446facccdc02a1a4ac55111556e0aa7090e4213b6ab07c6a1d0d2 | Python | 12,081 | 334 | # -*- coding: utf-8 -*-
"""
Created on Mon Jul 12 23:16:07 2021
@author: u0139894
"""
import cobra
import numpy as np
import os
import ast
class Reaction:
def __init__(self, model_folder=None, model_list=None, model=None, biochem_input=None, dbType=None, fixed_bounds=None):
'''
General class to ... |
481814fc878761164cbe69aac84e88f2a5c06e1d59fb077ad077f462ff7b0a5b | Python | 12,085 | 286 | """text_file
provides the TextFile class, which gives an interface to text files
that (optionally) takes care of stripping comments, ignoring blank
lines, and joining lines with backslashes."""
import sys
class TextFile:
"""Provides a file-like object that takes care of all the things you
commonly want to d... |
58388811842e3aa0d825bb41ed6f8a861e92929081f1ee7c319fe845d560a772 | Python | 12,087 | 304 | # 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... |
1b748918d48290daf630072cb7f5895eceae572c1ef7b9d6a73b440c1a9a3182 | Python | 12,088 | 303 | """
Set of utils for helping factory classes
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 16.09.14
"""
__author__ = 'martinez'
__version__ = "$Revision: 002 $"
try:
import graph
except:
import pyseg.graph
try:
import disperse_io
except:
import pyseg.disperse_io
#... |
42212f52e8c99efecb95931465ed458a9d39d01d40a1693cf3131a4ec3c5ac7f | Python | 12,088 | 251 | # Code adapted from the appyter-catalog github repository (https://github.com/MaayanLab/appyter-catalog/tree/main),
# distributed under an Attribution-NonCommercial-ShareAlike 4.0 International license.
# Librairies
import os
import pandas as pd
import numpy as np
import plotly
import plotly.graph_objs as go
from iter... |
c1ac88a2300cf4e6e95eddd56eaaed0ab189df506bb2a622ca58c98ed09a612b | Python | 12,088 | 275 | # 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... |
84e355d8bbe60a795c6215a6ba1f058e3e20716ab315fe5d10669c7ba1d56909 | Python | 12,090 | 294 | #!/usr/bin/python
# -*- coding:utf-8 -*-
# -*-mode:python ; tab-width:4 -*- ex:set tabstop=4 shiftwidth=4 expandtab: -*-
#
from ctypes import *
import sys
if sys.platform == 'linux2' or sys.platform == 'linux':
try:
dll = CDLL('/usr/lib/libgxiapi.so')
except OSError:
print('Cannot ... |
9a96fe8adedce659b4196a3127595d2c985c19d193b0ef7782514725163b9519 | Python | 12,090 | 313 | import time
from .pr2_utils import get_top_grasps
from .utils import get_pose, set_pose, get_movable_joints, \
set_joint_positions, add_fixed_constraint, enable_real_time, disable_real_time, joint_controller, \
enable_gravity, get_refine_fn, wait_for_duration, link_from_name, get_body_name, sample_placement, \... |
a668339407ab80f81fffea88768589dc5be5fec7a65f4db6bb85b2df912e0e78 | Python | 12,090 | 334 | import itertools
import logging
import numpy as np
from pyccg import chart
from pyccg.lexicon import predict_zero_shot, \
get_candidate_categories, get_semantic_arity, \
augment_lexicon_distant, augment_lexicon_cross_situational, augment_lexicon_2afc, \
build_bootstrap_likelihood
from pyccg.perceptron imp... |
e6047fcdff089734c67f7fb5a11ed4b2a007e02813d2825d20252c2eb14927ca | Python | 12,090 | 294 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 21 10:56:33 2022
@author: deeperthought
"""
GPU = 0
import tensorflow as tf
if tf.__version__[0] == '1':
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list="0"
tf.keras.backend.s... |
5609aef9898f28138ea5520697a6f8452435a9fd5e6f28eac1a40079c95dd7f4 | Python | 12,096 | 236 | import numpy as np
import math
import os
from neuron import h
import torch
import pickle
from eworm.ghost_in_mesh_sim.pre_interaction import CNN, CNN2
from eworm.network.detailed_circuit import DetailedCircuit
from eworm.utils import *
from eworm.network import *
class WormNeuralNetwork(object):
"""class for a wo... |
cb20ba624b6240d071d6ed1e9c8c4a76adabffafdcf3c91b59186ed86be0156d | Python | 12,098 | 453 | # import tensorflow as tf
import numpy as np
from tqdm import tqdm
import sys
import torch
import pickle
from sklearn.metrics import classification_report
def DF_train(model, dataloader, loss_func, device):
model.train()
# counter = 0
# loss_avg = 0
losses=[]
outputs=[]
y_real=[]
for x, y... |
da2c27733c0f277612dc9d0ad298827edadfd1e78e49ded78a41ce17c70e3af3 | Python | 12,100 | 313 | import os
import torch
import torch_sparse
import numpy as np
from itertools import combinations
import random
from utils.sampler import Adj
from torch_geometric.data import Data
from torch_geometric.transforms import ToSparseTensor
from torch_geometric.utils import remove_self_loops, to_undirected
def add_... |
6f4f0a30757534124f6180b981599ca016e04124bc3114934d4848c63bf49e3d | Python | 12,111 | 288 | """
BEFORE RUNNING
##### Manually assign corresponding labels from histological atlas
see `MicroarrayData/all_structure_lut.csv`
##### Reannotate microarray data
microarray probes reannotated (March 2023)
##### download latest biomart data (approved symbols for genes etc, April 2023)
https://biomart.genenames.org/mar... |
21239be06ea6398ae7cd5b42d4943f2e84fa4fd039786a1afd93cd0939646dc5 | Python | 12,112 | 331 | """Edge / gradient / connected-component utilities ported from MATLAB.
Functions here mirror the originals in `utils/`:
- canny_edge_magnitude <- canny_edge_histogram.m (the gradient-magnitude part)
- threshold_histogram <- threshold_Histogram.m
- canny_edge <- MATLAB's edge(I,'ca... |
6ff67123ab4cd157188cedbb47a7b014faeef5ff2e84665e36dc85fdfc98df8f | Python | 12,117 | 241 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat May 6 10:09:47 2023
@author: daltonm
"""
from pynwb import NWBHDF5IO
import ndx_pose
import numpy as np
import matplotlib.pyplot as plt
from importlib import sys
import neo
import elephant
from quantities import s
from os.path import join as pjoin
fro... |
1d4f576ccef4a3202ad1bb6f8372fc1256d8456f24ac4d9e7afba65f9dd58051 | Python | 12,118 | 324 | from __future__ import division
import logging
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from func_unsupervised_TC import fit
from IterativeMethod import iterativeTC
"""
Created on Mon Jun 24 16:04:07 2019
@author: Hannah Choi
"""
"""
This code finds intra- or inter-module h... |
8be014a0c841bcdebd798d6438dc3da0c85e23426cbeb4ed4bf443f6ec6fbfb1 | Python | 12,119 | 316 | # 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... |
5f040a931ea50779c5fa33c568d24a50599ce078c3ef7c7ec857bbd9b6424f70 | Python | 12,120 | 303 | # -*- coding: utf-8 -*-
import tensorflow as tf
from .. import _logging as logging
from .core import *
__all__ = [
'LocalResponseNormLayer',
'BatchNormLayer',
'InstanceNormLayer',
'LayerNormLayer',
]
class LocalResponseNormLayer(Layer):
"""The :class:`LocalResponseNormLayer` layer is for Local ... |
dbd804653227492e2d5b9db98e1ac5426830fe4b74f7f33ea11cb8615e49ba87 | Python | 12,120 | 400 | from __future__ import annotations
from collections.abc import Iterator
from dataclasses import dataclass
import numpy as np
from typing_extensions import Self
from SurvivalEVAL.evaluations.util import (
_inverse_censoring_weights,
check_and_convert_event_data,
validate_time_point,
)
from SurvivalEVAL.no... |
38a0687505089f6d86085ab8ecc344922e4c491e5d52aa456623af7c2a0db49f | Python | 12,121 | 304 | """
Multiclass test for unsupervised and deterministic classification of membrane-bound particles
Input: - The STAR file with the particles to classify
- Classification parameters
Output: - A set of STAR files with the new classes
- 2D rotational averaged around membrane normal e... |
1a2cab382a9d71f639c09ce8c87d2dc08d1d2baaebdaddaf7c2d8ee1a8208a2c | Python | 12,122 | 285 | import json
import re
import os
import time
import h5py
import numpy as np
import csv
from .kernel import NetOutInfo, DeepHE3Kernel
class testResultAnalyzer:
def __init__(self, data_dir, output_dir):
self.data_dir = data_dir
self.output_dir = output_dir
self.kernel =... |
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