sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3003aade817a14a9e8a61887a6a18e3c65abf3055170baa8390e2619ab971f02 | Python | 620 | 21 | import nibabel as nb
import numpy as np
dataFile = '/home/sebastian/Desktop/testRelativeResolution/patchFlatten/sub-06_ses-001_task-stim_run-001_T1w.nii'
dataArr = nb.load(dataFile).get_fdata()
dataArr.shape
dataArrFlat = dataArr.flatten()
dataArrFlat.size
newArr = np.arange(dataArrFlat.size)
dataArrFlat.size
newArr... |
7a90e7b02887f64c7e88fc6ae5678e290fb93ffe7c8be18ca12cb125c4e7dcb0 | Python | 620 | 24 | from pathlib import Path
from setuptools import setup, find_packages
with open('README.md') as f:
readme = f.read()
with open('LICENSE') as f:
license = f.read()
setup(
name='basenji',
version='0.1',
description='Sequential regulatory activity machine learning',
long_description=readme,
autho... |
d5ff366f3ad7e350e0b97a4e4bb6da9a3933203f2254f0c358585a8102fa8765 | Python | 620 | 33 | from .aqm import (
AQMgasDataset,
AQMsolDataset,
)
from .qm7x import QM7XDataset
from .materialscloud import (
AgClusterDataset,
AuMgODataset,
CarbonChainDataset,
NaClDataset,
)
from .md22 import DHADataset
from .water import MBPolDataset
from .dimers import DimersDataset
from .efa import (
... |
1b603621059a8cecd83ef38c986d7532da94c4885f28aaff28e298d43662ad39 | Python | 621 | 21 | from rdkit import Chem
def make_mol(s: str, keep_h: bool):
"""
Builds an RDKit molecule from a SMILES string.
:param s: SMILES string.
:param keep_h: Boolean whether to keep hydrogens in the input smiles. This does not add hydrogens, it only keeps them if they are specified.
:return: RDKit molecu... |
33447df3b8ac42da1f3a6b0f3b08b64223184310c92eae6bba2ac20f5e67858f | Python | 621 | 27 | import os
import logging
from threading import Thread
__version__ = '1.3.1'
try:
os.environ['OUTDATED_IGNORE'] = '1'
from outdated import check_outdated # noqa
except ImportError:
check_outdated = None
def check():
try:
is_outdated, latest = check_outdated('ogb', __version__)
if is_... |
923b3d353ea446ef135624c4297268e74d7daa139da2f7f0173e61245ca48e33 | Python | 621 | 21 |
import numpy as np
def gen_sample(hist, bins, scale='linear'):
random_sample = np.empty([0,1])
if scale == 'log2':
bins = np.log2(bins)
if scale == 'log10':
bins = np.log10(bins)
for b_ind, b in enumerate(bins[:-1]):
random_sample = np.concatenate((random_sample, (np.random.... |
2bc8e44c5fb56968e121c642e3a3c09559a2c6cb3c5dc3801c2e2852bf9fd503 | Python | 622 | 17 | import pytest
from qtpy import PYSIDE2
from tests.utils import pytest_importorskip
@pytest.mark.skipif(PYSIDE2, reason="Not available for PySide2")
def test_qtnetworkauth():
"""Test the qtpy.QtNetworkAuth namespace"""
QtNetworkAuth = pytest_importorskip("qtpy.QtNetworkAuth")
assert QtNetworkAuth.QAbstra... |
1ee5d42c77e53b38c60f165509eef1b7735e355ee24386d034be518d975e044a | Python | 623 | 20 | # -----------------------------------------------------------------------------
# Copyright © 2020 Marcin Stano
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
... |
2ed75abe5ce04e937c5b8f7c417d270966aaa84e3e8fc4af645c188598b9cff9 | Python | 625 | 14 | from brainscore_vision import metric_registry
from .metric import BootstrapDistributionSimilarity, NeuronalPropertyCeiling
metric_registry['ks_similarity'] = BootstrapDistributionSimilarity
metric_registry['property_ceiling'] = NeuronalPropertyCeiling
BIBTEX = """@article{marques2021multi,
title={Multi-scale hierar... |
4098276ad03021a4151cb690cd9d8e51e0f996f59bec1c95d424eda968ce9462 | Python | 625 | 19 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtMultimediaWidgets... |
42102fe125742e27200a0fdf4d2fa93bcf182473ff80f8621d7f91a599078926 | Python | 625 | 21 | import torch
import random
import numpy as np
def set_seed(seed, device_id='cuda:0'):
# Set seed for Python's built-in random library
random.seed(seed)
# Set seed for numpy
np.random.seed(seed)
# Set seed for PyTorch CPU
torch.manual_seed(seed)
if torch.cuda.is_available():
# Set ... |
aeefed587019317aa9df6272b24f3aee377aa16e047679c976d73ac16c800ab5 | Python | 625 | 18 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers, LAYER_NAME
_REGION_LAYER_MAP = {
'V1': LAYER_NAME,
'V2': LAYER_NAME,
'V4': LAYER_NAME,
'IT': LAYER_NAME,
}
model_registry['gabor_fil... |
2f20699e89d1a1e4926dc83300de8a611beffef0766b706991c955e6a23acb3a | Python | 626 | 23 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtConcurrent classe... |
401266e9cb1eec96b7e68a88fe31fa0e6028de2781928c3f4af1e6adb02fa0b1 | Python | 626 | 26 | import json
import numpy as np
def save_to_json(obj, file):
with open(file, "w") as f:
jso = json.dumps(obj, cls=NpEncoder)
f.write(jso)
def read_json(file):
with open(file, 'r') as load_f:
load_dict = json.load(load_f)
return load_dict
class NpEncoder(json.JSONEncoder):
de... |
6346ee1d3392e906c610ec6c1bd9b53d1fa6c0027df112e3e5d4806717070ad2 | Python | 626 | 40 | import numpy as np
from impedancefitter.single_shell import single_shell_model
omega = 2. * np.pi * np.logspace(0, 12, num=30)
# for single_shell_model
c0 = 1.
em = 10.
km = 1e-6
kcp = 0.5
ecp = 60
kmed = .1
emed = 80
p = 0.1
dm = 5e-9
Rc = 5e-6
# for double shell
Rn = 1.0
ene = 1.0
kne = 0.0
knp = 0.0
enp = 0... |
69db6708973ca3d44c9adb8da5d96303871806fe33b0614953695e3471747bc2 | Python | 626 | 18 | from argclz.commands import parse_command_args
from .main_active_place_cell import ActivePCOptions
from .main_cls_summary import ClsCellTypeOptions
from .main_motion_drift import MotionDriftOptions
from .main_neuropil_error import NeuropilErrOptions
from .main_trial_reliability import TrialReliabilityOptions
parse_com... |
904070c9880953040f86cc20fea5fa6b4825d6e42f9f95b155c3f164fa695281 | Python | 626 | 22 | import torch
import random
import numpy as np
def set_seed(seed, device_id='cuda:0'):
# Set seed for Python's built-in random library
random.seed(seed)
# Set seed for numpy
np.random.seed(seed)
# Set seed for PyTorch CPU
torch.manual_seed(seed)
if torch.cuda.is_available():
# Set ... |
e6bec8814a533679954c0f13000b975f845d630cb62fbd6baaf3a3923d911ed1 | Python | 626 | 20 | import platform
import sys
def ensure_supported_platform(
sys_platform: str | None = None,
machine: str | None = None,
) -> None:
"""Reject Intel macOS with a clear message during plugin discovery."""
current_platform = sys.platform if sys_platform is None else sys_platform
current_machine = platf... |
a909304f9940eb3e67ae16a60df694282ea44f7ad9141a12dd8cde4bdf33a86e | Python | 627 | 22 | #%%
from MixerUnetcopy import Rep_UNET_down, reparameterize_model
import torch
path = "/data1/home/ict08/skinseg/model_weights/segpc/repunet100/repunet100.ckpt"
save_path = "/data1/home/ict08/skinseg/rep_weights/segpc/repunet.ckpt"
a = torch.load(path)
class TPModel(torch.nn.Module):
def __init__(self):
s... |
09859635fe0cf8014bb6afb7f20481815c5e7b36ca9d3554ca5ced696d5224e3 | Python | 628 | 31 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
from core.core_definitions import simulation_timestep
from core.trace import Trace
class EulerTrace(Trace):
"""TODO"""
def __init__(self, size, tau):
"""TODO"""
super().__init__(size)
self.tau = tau
self.calculate_scale... |
41ed984bd880a213f5ae658ccccec3104e5f899b93b44164cde0f4a13ab523e1 | Python | 628 | 20 | #!/usr/bin/env python3
# Copyright (C) 2018-2022 Intel Corporation
#
# SPDX-License-Identifier: MIT
import os
import sys
if __name__ == "__main__":
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "cvat.settings.development")
try:
from django.core.management import execute_from_command_line
except... |
9310ebc4d117a8c9439edc1286929d125c5e01f9bc6743a07a0872ec6107e988 | Python | 628 | 18 | import math
import copy
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
def jackknife_est_error(model_list, samples):
'''Returns plotted data from mean standard error of coefficients for each model with error bars'''
c = np.concatenate([model.layers[0].coefficients for model in mo... |
a42ac61c0c041d75cab746f039018923f502f21ded41aeb666faa435f53292d9 | Python | 629 | 17 | TAGGED_ENTITY = '''
<mark class="entity" style="background: {color}; padding: 0.45em 0.6em; margin: 0 0.25em; line-height: 3; border-radius: 0.35em; box-decoration-break: clone; -webkit-box-decoration-break: clone">
{entity}
<span style="font-size: 0.8em; font-weight: bold; line-height: 3; border-radius: 0.35em... |
b2c5d9853c2efbe486ffc0c8c6b473c06fc2ed4eaf557f0c9c38bdb029b3b488 | Python | 629 | 25 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtNfc classes and f... |
b37b092346c0cef6bf32b789e0d71252486dce19fee06ea29d08328139b087fb | Python | 629 | 19 | #!/usr/bin/env python
# coding: utf-8
# Collapse barcode count by sample and known barcode
import sys
import pandas as pd
def count_barcodes(outdir, chunk_files):
if len(chunk_files) == 1:
df = pd.read_csv(chunk_files[0])
else:
df = pd.concat((pd.read_csv(x) for x in chunk_files), ignore_... |
b61948fb571b61e5ec84a5653129566fc4916b2d868fa66bd98839968645069f | Python | 629 | 24 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from django.apps import AppConfig
class WebhooksConfig(AppConfig):
name = "cvat.apps.webhooks"
def ready(self):
from django.conf import settings
from . import default_settings
for key in dir(default_settings):
... |
e98c6953c7c17658de83a8c917e9bd2a201c0ffe9da59074fbfa701e94826e85 | Python | 629 | 22 | from .data import data_matrix, design_matrix, heatmap, triangle_overlay
from .factor_embedding import factor_density, factor_embedding, factor_strip
from .loadings_heatmap import loadings_heatmap
from .loadings_scatter import loadings_scatter
from .loadings_state import loading_rank_diff, loadings_state
from .qc import... |
02b02194e26aa13827be747ac1638616e85ebf0d18cd3df60eb2aa81152b237e | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_1.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_1.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
1eea191246eeb208eb6628568a2f3ca77d04c06c4e9d2c41022abe140ac55894 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_5.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_5.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
45e6fe7209dae4c0f2acff22cca83a083f0cbeab1d54c046b43e7349cd96d8b8 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_7.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_7.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
540f6872392868d138c5634e8e74654077d7d42c81650c7f1dce9c529ccd73ba | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_6.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_6.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
a2577c71a862a2dd858444577bb0904753a35be378b9fceccd01b83697362973 | Python | 630 | 23 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtAxContainer class... |
b075aa3805e44e5ddbb93f00e6c5fcfe6e8e36a74d197eb9c38f48d62e791079 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_0.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_0.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
b0a89d048673f3188eca7129064d74be19a8d0831b775045f532ff76f181240e | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_3.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_3.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
b9d80abdb94642e6603032ff40e434700913c380e07ccee453ad01693cf04b48 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_4.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_4.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
bbc9206b0a128652e826dc2300561b4b8904ea1d607312bf16cc716af4cf8cf6 | Python | 630 | 22 | import numpy as np
import json
import pandas as pd
import csv
import sys
sys.path.append('..')
from utils.dataset import merge_and_split, simple_vectorize
def preprocess_dataset(dataset, server_id="209"):
train, valid, test = merge_and_split(dataset=dataset, server_id=server_id)
train_data, train_label... |
e525e7aed54ef4ed3da9269537cd78e8768735b90836f7f8f8a8bdff00eb98cf | Python | 630 | 25 | #!/usr/bin/env python
"""
Translate lists of space separated integers (magnitude less than 62) and print
as strings of alphanumeric characters. This is useful mainly for some machine
learning algorithms that only take string input.
usage: %prog < int_seqs > strings
"""
import sys
table = "012345678ABCDEFGHIJKLMNOPQ... |
fe1a17fe6f26d507ef5a6cfff41647f0fdfcf6566990a3be1a0bea844131b5e1 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_2.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_2.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
ff9e315ad33270b70b3fccc7abc302880b8ae8d4b0f64e6d100563f9d97ef0e5 | Python | 630 | 21 | import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
import ijson
import json
f1=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_8.json",'rb')
f2=open("/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-22/tweet_8.json",'rb')
out_file=open("/data2/whr/czl/TwiBot22-baselines/src/twi... |
5e63f57ca615d189a95938fea738cff502c108c03ce212bd769460b926f38f3c | Python | 633 | 24 | from collections.abc import Sequence
from eir.models.input.tabular.tabular import (
SimpleTabularModel,
SimpleTabularModelConfig,
)
def get_tabular_model(
model_init_config: SimpleTabularModelConfig,
cat_columns: Sequence[str],
con_columns: Sequence[str],
device: str,
unique_label_values:... |
732fd8788aaa13179a094805770f952210f104bd77eab0e9ee4b4d4787249709 | Python | 633 | 22 | import pytest
from qtpy import PYQT5, PYSIDE2
@pytest.mark.skipif(PYSIDE2 or PYQT5, reason="Not available in PySide2/PyQt5")
def test_qtopenglwidgets():
"""Test the qtpy.QtOpenGLWidgets namespace"""
from qtpy import QtOpenGLWidgets
assert QtOpenGLWidgets.QOpenGLWidget is not None
@pytest.mark.skipif(P... |
e1f86c7038dd7631f23572eb2f18b4bceffb508e79ed8f2d5c8d43768e6bcb15 | Python | 633 | 27 | import unittest
import arbor
from . import fixtures
_mpi_enabled = arbor.__config__
@fixtures.context()
def skipIfNotDistributed(context):
skipSingleNode = unittest.skipIf(
context.ranks < 2, "Skipping distributed test on single node."
)
skipNotEnabled = unittest.skipIf(
not _mpi_enabled,... |
21aa63e7552e910b603d0b263e25f6102eccc8488297ec7d8787f4fe603d0db9 | Python | 634 | 20 | import datetime
def time_to_str(timestamp: int) -> str:
"""
Convert seconds past Epoch to human readable string.
"""
datetimestamp = datetime.datetime.fromtimestamp(timestamp)
return '{:04d}-{:02d}-{:02d}-{:02d}-{:02d}-{:02d}'.format(
datetimestamp.year, datetimestamp.month, datetimest... |
877ee02badb289f69948a94ff0e4d63fb3ab7f99935dacd798a80acf2364dd6c | Python | 634 | 24 | import torch.nn as nn
from ..ops.normalization import pixel_norm
__all__ = ['PixelNorm']
class PixelNorm(nn.Module):
def __init__(self, dim=1, eps=1e-8):
"""Pixel normalization.
References:
- https://papers.nips.cc/paper/2012/file/c399862d3b9d6b76c8436e924a68c45b-Paper.pdf ("Local Re... |
909fda1d615bb235186e54771ae6e2a12f7dd94108a9a119e43913bff76729b8 | Python | 634 | 25 | import pandas as pd
label = pd.read_csv('/data2/whr/czl/TwiBot22-baselines/datasets/Twibot-20/label.csv')
user = pd.read_csv('./user_feature.csv')
user_list = list(user['id'])
del_list = []
bool_label = []
for i,r in label.iterrows():
if r[1] == 'human':
bool_label.append(1)
else:
bool_label... |
24cfb7995c189e28cc03e9f35aabd1f4292888b61558a481bb26b15c38a6bf91 | Python | 635 | 24 | # Copyright (C) 2021-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from django.contrib.auth.models import AbstractUser
from django.db import models
class UserCreationMethod(models.TextChoices):
"""How the account's credentials were first established."""
REGISTRA... |
2f0cc9b03e3f62d43538bf0b4d96e3bd42126d582682518fc322606dce20bb2f | Python | 635 | 25 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
requirements = [ "torchvision",
"torch"
]
setup(
packages=find_packages(exclude=['tests']),
include_package_data=True,
install_requires=requirements,
license="MIT license",
zip_safe=False,
... |
465eb8c480836757ee22ed6ba5c8c39e198d12f9323dfe5b2054c120ad0ec864 | Python | 635 | 23 | def _get_version():
"""Get version from package metadata (generated from pyproject.toml
during installation)."""
try:
from importlib.metadata import PackageNotFoundError, version
return version('pyment')
except PackageNotFoundError:
import os
import tomllib
pyp... |
bfead92b856912c055305be0b3ad9823fa7852d20b2d2f2af7ef473cc6dd5d18 | Python | 635 | 22 | """Test the deferred import error mechanism"""
# See https://github.com/spyder-ide/qtpy/pull/387/
import pytest
from qtpy import QtModuleNotInstalledError
def test_missing_optional_deps():
"""Test importing a module that uses the deferred import error mechanism"""
from . import optional_deps
assert ... |
69cc2da2ece892f97ab2c6e458af4a6feb0589d083608c9f6059cebdc612e80e | Python | 636 | 25 | import pandas as pd
label = pd.read_csv('/data2/whr/czl/TwiBot22-baselines/datasets/cresci-2017/label.csv')
user = pd.read_csv('./user_feature.csv')
user_list = list(user['id'])
del_list = []
bool_label = []
for i,r in label.iterrows():
if r[1] == 'human':
bool_label.append(1)
else:
bool_lab... |
92a5d756af7750428847bb65ab75be5f6a354881d5175385786db8ccf20285d4 | Python | 636 | 25 | import pandas as pd
import numpy as np
import seisbench.data as sbd
def test_spectrum_dataset(data_dir):
data = sbd.SpectrumDataset(
data_dir / "esm_spectrum_example/",
component_order=(
"acc_mp_u",
"acc_mp_v",
"acc_mp_w",
"dis_mp_u",
"d... |
d5ab0caf7c78d46ad279de570853577cca0585a42a1bf93d6ad2f71573beb8f1 | Python | 636 | 25 | import pandas as pd
label = pd.read_csv('/data2/whr/czl/TwiBot22-baselines/datasets/cresci-2015/label.csv')
user = pd.read_csv('./user_feature.csv')
user_list = list(user['id'])
del_list = []
bool_label = []
for i,r in label.iterrows():
if r[1] == 'human':
bool_label.append(1)
else:
bool_lab... |
280f16d66afae72e1edf6c8d5e1f82e5c895b6253bfc7ae9defea7a5a3ed22d3 | Python | 637 | 27 | from abc import ABCMeta
class Loop(metaclass=ABCMeta):
"""Abstract base class that represents a loop.
Could be spatial or temporal loop.
"""
def __init__(self, dimension, size) -> None:
"""Initialize this Loop object.
Args:
dimension (str): The dimension, e.g. "K"
... |
ffe908b9aaa5590455f3ecd786d60aee7c26693bfff4e47c1fd7fe0a4ddfa59b | Python | 637 | 31 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
from core.core_definitions import simulation_timestep
from core.trace_2d import Trace2D
class EulerTrace2D(Trace2D):
"""TODO"""
def __init__(self, size, tau):
"""TODO"""
super().__init__(size)
self.tau = tau
self.calcul... |
93fc98204849d2d54de533bdc93ccff4da1c69e3881a43fe2486241e07ba6bbe | Python | 638 | 20 | import os
import random as rn
import numpy as np
import tensorflow as tf
def enforce_reproducibility(seed=2023):
# Check PYTHONHASHSEED
current_seed = os.environ.get("PYTHONHASHSEED")
if current_seed != "0":
raise EnvironmentError(
"PYTHONHASHSEED must be set to '0' for full reproducibi... |
a153629cbcd56f586cb1ab57ba5e64643f90dc76d736239ee91f232c0bdd4cc8 | Python | 638 | 24 | # Generated by Django 4.2.13 on 2024-07-12 19:01
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("engine", "0079_alter_labeledimageattributeval_image_and_more"),
]
operations = [
migrations.AlterField(
... |
fb3d6bc943cf2b6225ff4e8d06abea3bfd8e7f53fb3d6f72a8444e5ed71fdc6b | Python | 638 | 23 | import sys
import pytest
from qtpy import PYQT6, PYSIDE6
from tests.utils import pytest_importorskip, using_conda
@pytest.mark.skipif(
PYQT6 or PYSIDE6,
reason="Not available on Qt6-based bindings",
)
@pytest.mark.skipif(
sys.platform != "darwin" or using_conda(),
reason="Only available in Qt5 bindi... |
01557f70cf06509c8ce25772ac2cd611b718829dd427e43a51a94cb036ce8f81 | Python | 639 | 19 | """The only production construction site for the Codex client.
Codex keeps its own loader (``load_codex_model``) with its subscription
authentication. This builder is the sole call site: the endpoint packs the
loader's arguments into ``client_kwargs`` and hands them here.
"""
from __future__ import annotations
from ... |
30751cf129d41fe774e7004413b770a8fe7386bf46a7e5acd9967da130a6f51c | Python | 639 | 23 | #!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
from python.segmentation.FileIO import plotParameters
def parse() -> Nam... |
32582d29d7cf7ebd0106795e5837b48e8e1e3c929877f39cdba7ca11196f7574 | Python | 639 | 21 | import numpy as np
from brainways.pipeline.tps import TPSTransformParams
from brainways.project.info_classes import BrainwaysParams
from brainways.ui.controllers.cell_3d_viewer_controller import Cell3DViewerController
def test_enabled_false_by_default():
params = BrainwaysParams()
enabled = Cell3DViewerContr... |
c14f6909dc7160166d73832f10d496b9fb346b399109c3959cdf42f594f45124 | Python | 640 | 33 | #!/usr/bin/env python3
# coding: utf-8
import json
import math
import nrn_validation as V
V.override_defaults_from_args()
# dendrite geometry: 100 µm long, varying diameter.
length = 100.0
npoints = 200
def radius(x):
return math.exp(-x) * (math.sin(40 * x) * 0.05 + 0.1) + 0.1
xs = [float(i) / (npoints - 1)... |
ecbce1f03fa275cb361c90454e2508cfc218e0aa037a674379730c5838380b1a | Python | 640 | 17 | import SimpleITK as sitk
import numpy as np
import dask_image.imread
import skimage.io as skio
def convert_16_to_8(image_path, save_path):
im_arr_16 = dask_image.imread.imread(image_path)
im_sitk= sitk.GetImageFromArray(im_arr_16)
im_sitk_8 = sitk.Cast(sitk.RescaleIntensity(im_sitk), sitk.sitkUInt8)
im... |
c3875d82aa1cc0380f1077de4711a8f3cc34c87eabf7417b134d0f441b051e67 | Python | 641 | 18 | import OptimalBattery.simulate as sim
import os
# Make a random task battery with 100 task
D = sim.sim_connectivity(num_task_lib = 100,
n_parcels = 5,
n_voxels_y = 100,
n_sim = 100,
battery_sizes = [3,4,5,6,7,8,9,10,11,12,13,14,15,16]... |
3ceaa6944e08b174317c49620c8e32b7ab61c2df9d557c76d3f50b943a90c19c | Python | 642 | 20 | import importlib
def create_instance(class_path: str, *args, **kwargs):
"""
Dynamically creates an instance of a class given its full path.
Args:
class_path (str): The full path to the class, e.g., 'module.submodule.ClassName'.
*args: Positional arguments to pass to the class constructor.... |
667bb04449f950aa396c9acbeef8fd0622cde9a8b9d3c1507cd8a00066c864aa | Python | 642 | 23 | import logging
from importlib.metadata import PackageNotFoundError, version
from osl_dynamics.config_api.pipeline import run_pipeline
from osl_dynamics import meeg
# Setup the version
try:
__version__ = version("osl-dynamics")
except PackageNotFoundError:
__version__ = "unknown"
finally:
del version, Pack... |
8540f58c79d1abb6db189b9a27af3746f6cf6ed3d61ff5ade08c5efc679d5b1b | Python | 642 | 13 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or... |
e31288137be70d99ddafa5caf06beba4e4fe98e5fa6e4a3d294fc3b1fce7c439 | Python | 642 | 34 | #!/usr/bin/env python
"""
Read a PAIRWISE maf from stdin and print the fraction of columns whose bases
match for each alignment.
TODO: generalize for more than two speceis.
usage: %prog < maf > out
"""
import sys
from bx.align import maf
def __main__():
maf_reader = maf.Reader(sys.stdin)
for m in maf_re... |
fbbcaf7596e26ebc7dc09acbb04cb2df90fb638e9866997ac24dc4d8d90f12cd | Python | 642 | 23 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtQuickControls2 cl... |
f086038cd01178d358fb81e16dde0afb3fec1d533ac5f4fc8a9f92ee335e788c | Python | 643 | 26 | import os
from pathlib import Path
base = Path("/data2/whr/czl/TwiBot22-baselines/src")
datasets = os.listdir(base)
def has_markdown_file(files):
for file in files:
if file.endswith(".md"):
return True
return False
excluded = ["utils", "simple_GNN", "simple_NN", "simple_svm", "template_m... |
c47d5fae325146511db41c49b1e6c8609d451ead61379ddb3252fffbe1da61f1 | Python | 644 | 21 | """
This module is an example of a barebones sample data provider for napari.
It implements the "sample data" specification.
see: https://napari.org/stable/plugins/guides.html?#sample-data
Replace code below according to your needs.
"""
from __future__ import annotations
import numpy
def make_sample_data():
""... |
d221e30959a982b7568890ddbadc470a149025f0e59f29a20ac21267d66dd9ca | Python | 644 | 15 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or... |
fa07a043d92c1f9735ef8cf45e0135316de3d1e0c2e3f0e44592cacd83170024 | Python | 644 | 22 | import subprocess
import sys
import yaml
script = 'SOM/clusterSOM/plot_psth_and_zeta.py'
scripts = [script]#
pathpath = 'PATHS/filepaths_carlen.yml'
with open(pathpath, 'r') as myfile: pathdict = yaml.safe_load(myfile)
sys.path.append(pathdict['code']['workspace'])
from pfcmap.python import settings as S
setkeys = ... |
01753ad49d30ec6a1c0c1a94c31265d3e886a82c5ea485ee042e34b5e094d0db | Python | 645 | 22 | """
Cumulate quantities, keep counts, and retrun averages
"""
from collections import defaultdict
class Cumulator:
"""
Cumulate quantities, keep counts, and retrun averages
"""
def __init__(self):
self.total = defaultdict(float)
self.count = defaultdict(int)
def update(self, new_da... |
1adf23879c0b237362a6ad158b5d864309fcd2113c142a1fb69de4e12d40dbd1 | Python | 645 | 33 | """
Module to train a bioFAM model
"""
import scipy as s
import pandas as pd
import numpy as np
from mofapy2.core.BayesNet import BayesNet
def train_model(model):
# Sanity check on the Bayesian Network
assert isinstance(model, BayesNet), "'bayesnet' has to be a BayesNet class"
####################
... |
3d4e4efe7c04bcb1dbb26cd6d21ef6280273bb6c0c409549b5275c8bdc8309ee | Python | 645 | 20 | from pathlib import Path
import fire
from brainscore_vision import score as _score_function
def score(model_identifier: str, benchmark_identifier: str, conda_active: bool=False):
result = _score_function(model_identifier, benchmark_identifier, conda_active)
print(result) # print instead of return because f... |
8b0852b4c9388a90dba203bf8a34cafe9dac35eb485ec9dccf05ecb93570128f | Python | 645 | 19 | """The only production construction site for the Groq client.
Groq keeps its own loader (``load_groq_model``) with its API-key handling and
retry-on-auth logic. This builder is the sole call site: the endpoint packs the
loader's arguments into ``client_kwargs`` and hands them here.
"""
from __future__ import annotati... |
cb20192cfe000382af3b75dbc9f33e2738d5678bd8afb12c02d56e6a5c28c565 | Python | 645 | 27 | import torch
from torch import Tensor
import torch.nn as nn
from typing import List, Union, Tuple
class LSDModel(nn.Module):
def __init__(self, backbone: nn.Module):
"""
A model for predicting LSD's or Affinites for segmentation. Applies a sigmoid after the
output of the backbone!
... |
5e23384851c8fc69f823d875c7072317cf556635ecb1847d446c0fbe6aa73638 | Python | 646 | 18 | # Copyright 2024 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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... |
96fd0f0e765602276aeed01504cf71c6b471f08866efbb5c2734fc61cec3d4c9 | Python | 646 | 17 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from django.db.models.signals import post_save
from django.dispatch import receiver
from cvat.apps.consensus.models import ConsensusSettings
from cvat.apps.engine.models import Task
@receiver(post_save, sender=Task)
def __save_task__initialize_con... |
c184ab474c448396b3a8a7bcb5dbb53d06a244060b6d1a8c85ffb9bfe21ec751 | Python | 646 | 29 | # Generated by Django 4.2.26 on 2026-05-05 18:39
from django.db import migrations
class Migration(migrations.Migration):
dependencies = [
("engine", "0100_alter_task_mode"),
]
operations = [
migrations.AlterModelOptions(
name="labeledimage",
options={},
)... |
8dbce9a86e2f3c3e004ba07f01111dbe523c6774b2ba3eba096fed5e1160a654 | Python | 647 | 26 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
requirements = [ "torchvision",
"torch",
"gdown"
]
setup(
packages=find_packages(exclude=['tests']),
include_package_data=True,
install_requires=requirements,
license="MIT license",
zip_s... |
04413f172e1c749ca39977d61f934f9b98837a3613f5dd00e0da725b6c824248 | Python | 648 | 24 | import pytest
import warnings
from ase import Atoms
# Configure pytest-asyncio
#pytest_plugins = ("pytest_asyncio",)
@pytest.fixture(autouse=True)
def setup_test_env():
"""Setup any test environment variables or configurations needed"""
# Filter numpy deprecation warnings
warnings.filterwarnings(
... |
26690865aefa1f31ba9cec309cb9897b48f74ed4374be347720938a359627891 | Python | 648 | 22 | """A sub-package containing IO-related modules for storing intermediate results of operations performed by instances of
:py:class:`~corelay.processor.base.Processor`. This can be used in a :py:class:`~corelay.pipeline.base.Pipeline` to prevent the re-computation of
intermediate results needed multiple times, or as a ca... |
43ba4522fcc8ca8c2dd07fd4cd6f3116bc5c31a8338b214193cbf5cf3d588dba | Python | 648 | 14 | class Test_RVC_Config:
def test_config(self, demo_dir,dropConfig):
assert dropConfig.RVC.getWorkdir() == demo_dir + "/Scripts/rnaVariantCalling/pipeline"
dict_ = {
'groups': ['batch_0','batch_1'],
'highQualityVCFs': [f'{demo_dir}/Data/high_confidence_snps.vcf.gz', f'{demo_dir... |
562d7a5f738cbb980a79869e9d1931927a77299c51250d4a0d8b7d4db3ced15a | Python | 648 | 20 | import ast
import pytest
import numpy as np
import impyute as impy
SHAPE = (5, 5)
@pytest.mark.filterwarnings('ignore::FutureWarning')
def test_output_file_exists(test_data, results_path):
data = test_data(SHAPE)
labels = np.array([1, 0, 1, 1, 0])
imputed_mode = []
imputed_mode.append(["mode", (impy.... |
8517023812f934c9e5deb799db77316cd95488d559b68b6ddd35782b6dc6cee4 | Python | 648 | 33 | # Source: https://github.com/neuraloperator/neuraloperator/blob/main/neuralop/data/transforms/base_transforms.py
from abc import abstractmethod
import torch
class Transform(torch.nn.Module):
"""
Applies transforms or inverse transforms to
model inputs or outputs, respectively
"""
def __init__(se... |
e21589c347b7f0bb0a5e2e2ba68d7802e4a06f51446151f05e608a4f17f230fb | Python | 648 | 15 | import warnings
from .atlas_centric_preprocessor import AtlasCentricPreprocessor
from .native_space_preprocessor import NativeSpacePreprocessor
# Deprecation warning for Preprocessor alias, added to ensure backward compatibility.
class Preprocessor(AtlasCentricPreprocessor):
def __init__(self, *args, **kwargs):
... |
3fe789330cfd9380a7311b73dc3bdd76179436b33093f22051d53e237562c950 | Python | 649 | 25 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides QtQuick3D classes a... |
820b0656d7e4a6ea40ef17abad65d4e26dea15dadc2157d04af0138e61139d9f | Python | 649 | 29 | import numpy as np
from scipy.special import j1
def airy_disk(diff_lim):
"""
Creates a PSF defined by the Airy disc
Parameters:
diff_lim: the full width half-max (FWHM) of the PSF
Returns:
psf: a numpy array of size [N,N] with the PSF
"""
L1 = diff_lim*(0.61/0.5)
u = in... |
ff885b11424f47b633d635ef2c25b3e5a2f6ba2240df71a378407fc30297c027 | Python | 649 | 25 | from abc import ABC
from pathlib import Path
from typing import Optional, Tuple
from brainways.utils.image import Box, ImageSizeHW
class ImageReader(ABC):
def __init__(self, path: Path, scene: int):
self.path = path
self.scene = scene
self.scene_bb: Optional[Box] = None
def read_imag... |
7f1e5df6e5510934dc4e522328c9e3526fd805f3a8ef3f6e5730a66334f48e2b | Python | 651 | 32 | #!/usr/bin/env python
"""
Read a file containing a 0 or 1 on each line (`feature_file`), output
all lines from stdin for which that value was 1
TODO: no need to read the feature_file into memory here, just iterate in
parallel.
usage: %prog feature_file < ...
"""
import sys
def __main__():
feature_file =... |
87ca4a5580e207d1c4bc49fd784a04c8ba96bf9a0c7717c50554185e7775f85b | Python | 651 | 17 | from chemgraph.state.graspa_state import PlannerResponse
def test_graspa_planner_response_accepts_bare_task_list():
payload = [{"task_index": 1, "prompt": "Run worker batch 1."}]
parsed = PlannerResponse.model_validate(payload)
assert parsed.next_step == "executor_subgraph"
assert parsed.tasks[0].task... |
e652259e3c3f38a94480d25bdfd0b93a89b720b949ccfdc115a8976fa85271bf | Python | 651 | 19 | """The only production construction site for the Ollama client.
Ollama keeps its own loader (``load_ollama_model``) with its curated-catalog
validation. This builder is the sole call site: the endpoint packs the loader's
arguments into ``client_kwargs`` and hands them here.
"""
from __future__ import annotations
fro... |
175e02e09bcbdb8a9d962c78f6bf38b47819f49cea404157d21953dd16c5c1b2 | Python | 652 | 18 | from .eqtransformer import EQTransformer
from .phasenet import PhaseNet
def PickBlue(base: str = "phasenet", **kwargs):
"""
Initialize a PickBlue model. All `kwargs` are passed to `from_pretrained`.
:param base: Base model to use. Currently, supports either `eqtransformer` or `phasenet`.
"""
if b... |
b1d7cf3716ae8805c50abf73750f353d4878a7bfcfb4a01443565188bdcb3149 | Python | 652 | 19 | import chromatics
import io
import pandas as pd
import subprocess
def samtools(arguments):
cmdline = 'samtools {}'.format(arguments)
p = subprocess.Popen(cmdline, shell = True, stdout = subprocess.PIPE)
stdout, _ = p.communicate()
return chromatics.read_bed(io.StringIO(stdout.decode('utf-8'))).set_inde... |
4b2ee276ba885cf368247b022008379b5611aa523cbaf8c923dd2984216cdefa | Python | 653 | 20 | from argclz.commands import parse_command_args
from .cache_ctype_cord import CellTypeCordCacheBuilder
from .main_cls import ClsTopoOptions
from .main_cords import RoiCordOptions
from .main_fov import FOVOptions
from .main_spatial_topo import SpatialTopoPlotOptions
from .main_visual_topo import VisTopoPlotOptions
parse... |
025446e5272e9e369522d70d63fb5f9f46758d725e0740a5319e624db57775c2 | Python | 655 | 37 | # imagecodecs/__init__.py
from __future__ import annotations
from .imagecodecs import ( # jpeg_check,; jpeg_version,; JpegError,; JPEG,
NONE,
NUMPY,
DelayedImportError,
NoneError,
NumpyError,
__all__,
__dir__,
__doc__,
__getattr__,
__version__,
_codecs,
_extensions,
... |
0f7e903caf713fcae3bc62d61cf5c7ac346d2bb442ae10ef80445a872498a36a | Python | 655 | 27 | #!/usr/bin/env python
"""
Read TFLOC output from stdin and write out a summary in which the nth line
contains the number of sites found in the nth alignment of the input.
TODO: This is very special case, should it be here?
"""
import sys
from collections import defaultdict
counts: dict[int, int] = defaultdict(int)
... |
1a6059529c889badcc8bcf9d2c8516ec0dff943e1880d090d70f8b48f0fe7da3 | Python | 655 | 21 | from matplotlib import pyplot as plt
untreated = [21, 3, 30, 25, 31, 13]
treated = [2, 10, 1, 10, 17, 23]
labels = ["Sparse", "Swollen","Tubular", "Mixed", "Bent Lamellar", "Orthogonal Lamellar"]
untreated = [i/sum(untreated) for i in untreated]
treated = [i/sum... |
7011b1d2970b4200e395b2f7bc9f6074e982893acadf581b44df090285b634f3 | Python | 655 | 23 | from pathlib import Path
from typing import Union
from brainways.utils.image import ImageSizeHW
from brainways.utils.io_utils.image_path import ImagePath
from brainways.utils.io_utils.readers.qupath_reader import QupathReader
def get_scenes(filename: Union[str, Path]):
reader = QupathReader(filename)
return ... |
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