sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
da280f9f23b13af905e360bd7573b3d713ca7ccc8c5b4a44b431cc543be58f23 | Python | 12,576 | 409 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 12 14:08:23 2018
@author: johan
"""
import mne
import numpy as np
import matplotlib.pyplot as plt
import copy
import pdb
import scipy
import struct
import json
import re
def convert_eeg_marker_meta_to_mne(fbase):
fhe=open(fbase + '.eeg'... |
87f3880c260e828791b48f5e101b52678ede1fd543cf8e2cfbd2352d32e1ca25 | Python | 12,577 | 301 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..modules.module import Module
class StandardUNet(Module):
"""
Standard UNet based on Paper https://arxiv.org/abs/1505.04597 .
:param in_channels: number of input channels (1 in standard configuration)
:param out_channels: numbe... |
9b337da31039be7c12776281a7f8f550ffced3e1c0206569d04965f201f7cce9 | Python | 12,577 | 259 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
9f570506a4e72c873100e0a564c80e06a10b8c48f280304f67dcfe43b834a954 | Python | 12,580 | 346 | from __future__ import absolute_import
import logging
import os.path
import re
from pip._vendor.packaging.version import parse as parse_version
from pip._vendor.six.moves.urllib import parse as urllib_parse
from pip._vendor.six.moves.urllib import request as urllib_request
from pip._internal.exceptions import BadCom... |
df6f2b9368aa78fb04fd7aa33bbdcb2f67442f9a0616510e73ed171561a8f8d3 | Python | 12,588 | 348 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Confound matrix selection based on Ciric et al. 2007."""
import os
import warnings
from pathlib import Path
import numpy as np
import pandas as pd
from nipype import logging
from scipy.signal import bu... |
cff44774ce6a137b40171420aacbd79bfd6d8e74711362a52f8f12d041699767 | Python | 12,593 | 402 | """
FormDefinition and field factories
"""
# TODO: A FormDefinitionField is closely linked to a form_builder result.
# Can this functionality be further abstracted and merged with form_builder?
from galaxy.model import (
FormDefinition,
FormDefinitionCurrent,
)
from galaxy.util import string_as_bool
FORM_TYPE... |
19bbe54806872ccce78f637abc505b022506dcb112d43daf676eb5a38853478e | Python | 12,594 | 266 | import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torch.utils.dat... |
08f808dcfe954a31730d13b5131bc1f4cd2321c3978c3ef2cd6af66efe8ef6c6 | Python | 12,596 | 305 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in April 2022
@author: Simon Delarue <sdelarue@enst.fr>
"""
from typing import Iterable, Optional, Union
from collections import defaultdict
import numpy as np
from scipy import sparse
from sknetwork.classification.metrics import get_accuracy_score
from sknet... |
1cfc86e8b77f4fd32f74dca0cff951c83a4ba287c19ee4e07ef3d5b7263db252 | Python | 12,597 | 321 | """Regression tests for r18l viz-plots + rank layout + graph caption findings.
Covers:
- H10 caption ``[:-2]`` left ``</FONT`` unterminated -> GraphvizRenderError on
any ``_has_direct_writes=True`` trace.
- M4 rank ``_compute_topological_layout`` sibling order depended on set/hash
iteration -> nondete... |
493665c0e466396d053f6f424bdf1c5c3fa19b8c4fc447d22d6f3abbecfcd192 | Python | 12,600 | 339 | # SPDX-License-Identifier: LGPL-2.1-or-later
from __future__ import print_function, division, absolute_import
import unittest
from collections import OrderedDict
import numpy as np
from pyEcoHAB import cage_visits as cv
from pyEcoHAB import sample_data, data_path
from pyEcoHAB import Loader
from pyEcoHAB import Timeli... |
f3df53c6dac16ab89546103ff5251a5f052497b1610e066331cddabb8b7b5677 | Python | 12,600 | 326 | # 2020.11.06-Changed for building GhostNetV2
# Huawei Technologies Co., Ltd. <foss@huawei.com>
"""
Creates a GhostNet Model as defined in:
GhostNet: More Features from Cheap Operations By Kai Han, Yunhe Wang, Qi Tian, Jianyuan Guo, Chunjing Xu, Chang Xu.
https://arxiv.org/abs/1911.11907
Modified from https:/... |
ca09b33d72bd774fe25575803e8024c5a54f8ef21ccfdceba5a02950d4e591aa | Python | 12,601 | 514 | """Miscellaneous compact reimplementations for dependency-gated targets."""
from __future__ import annotations
import torch
import torch.nn as nn
import torch.nn.functional as F
class FedProxCNN(nn.Module):
"""Small MNIST CNN commonly used with FedProx/FedAvg experiments."""
def __init__(self, classes: int... |
649dd6be66e5f29591a170121b604018d50c45af9b8e23dbdc9a0d52d3866c50 | Python | 12,603 | 302 | """AUD-CODE 2.12 (lane W051-SEMANTIC): half-precision norm reconstruction.
The shared norm linearization (``torchlens.semantic._norm_reconstruction``)
recomputed a norm in the PAYLOAD dtype -- five bf16 roundings -- while the
reconstruction tolerance model (``torchlens.semantic.tolerances``,
``RECONSTRUCTION_ULP_HEADR... |
22c7979d3e839a50574e20945939ac6844600ab195a9bb20515fa67bebcc96c9 | Python | 12,604 | 348 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""
Module providing generic info file proxy.
Author:
Mateusz Kruszyński <mateusz.kruszynski@gmail.com>
"""
import xml.dom.minidom
from . import signal_exceptions
from . import signal_l... |
e43ea8bff3a98953f6c0d783fadfbbd3bf9c7a24858eed07e66f1893eabbdbd6 | Python | 12,605 | 265 | import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torch.utils.dat... |
08fe1003befd877fc1e51b3d58c8b92e1d6eb96106c219d691abe13c0ea60446 | Python | 12,606 | 310 | """A set of functions for checking an environment details.
This file is originally from the Stable Baselines3 repository hosted on GitHub
(https://github.com/DLR-RM/stable-baselines3/)
Original Author: Antonin Raffin
It also uses some warnings/assertions from the PettingZoo repository hosted on GitHub
(https://github... |
606b297b26e593be7f44ce8e035401e8fc41c75d3a14126386e15deb06eca2e0 | Python | 12,609 | 347 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
controllers:
arm_controller : 7 joints, arm1: 0.07-2.67, arm2: -1.5-1.02, arm3: -3.46-1.5
arm4: -0.32-2.28, arm5: -2.07-2.07, arm6: -1.39-1.39
arm7: -2.07-2.07
... |
4e5e065fd83abcdc08b5ebed66936e0c29e2c1d5015a68d951546b8ee75f0f69 | Python | 12,612 | 370 | # Copyright 2025 Google.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, soft... |
a710eca47ce09df082fc387c6a05cacf41113569505c87ad276ff42417ac5a1c | Python | 12,615 | 287 | # pylint: disable=line-too-long,too-many-lines,missing-docstring,arguments-differ,unused-argument
import mxnet as mx
from mxnet import init
from mxnet.gluon import nn
from mxnet.gluon.nn import HybridBlock
from gluoncv.model_zoo.googlenet import googlenet
__all__ = ['inceptionv1_ucf101', 'inceptionv1_hmdb51', 'incepti... |
0a5d1822f82c3225b9533d9cd8ae2c380a356999a1e9360539a443a628465134 | Python | 12,617 | 235 |
from src.cfg import *
sys.path.append('')
from src.utils import *
from src.neuron_morphology import NeuronMorphology
import src.convertAllenSpace as CAS
class NeuronPopulation:
"""Class to manage and extract statistics from a population of neurons."""
def __init__(self, data_path: str, res: int):
"... |
95966a5dabf12f3a3804ec790b038e9e559d2ef72b65a867bb79421e4a9a7898 | Python | 12,618 | 343 | """
This module is an adapted version of the spiking neural network model of the saccade
generator in the reticular formation, originally developed by Anno Kurthwith support from Sacha van Albada.
The original work can be found at https://github.com/ccnmaastricht/spiking_saccade_generator.
Adaptations were made to i... |
062276d388b97aaa57105e2f08d13136d864ee82a4562aa44f3f0241b489e079 | Python | 12,619 | 333 | # -*- coding: utf-8 -*-
import logging
import os
import tempfile
import numpy as np
from dipy.io.stateful_tractogram import StatefulTractogram
from dipy.io.streamline import load_tractogram
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
from scilpy.tractograms.streaml... |
7683715a8a5bc8815e0108c61b5cafdef3ec9146981358ab6831ee7ca1cf7b1c | Python | 12,619 | 344 | """``tl.validate`` save options: ``output_device`` and ``save_budget``.
The validator capture saves every activation; these keywords give it the
capture API's own save options (same names, values, and defaults as
``CaptureOptions``) so a GPU model can validate with its activations held in
host memory. The CUDA tests a... |
5d072ed5355bd08cc81ca75842869d1e7b836720e3dadeb067266c6847bf9157 | Python | 12,624 | 316 | #!/usr/bin/env python3
"""plot_matches.py
Top level command-line interface for generating plots related to the
wafer section order solving.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU Ge... |
8afc00118d24afcd536ce283b2aa7fe0bbd85fa5af803e5e2be7eec2dbf9edc9 | Python | 12,626 | 272 | from typing import Literal, List
import numpy as np
import pandas as pd
from difflib import get_close_matches
import tensorflow as tf
# print("tf.version: ", tf.version.VERSION)
# print("tf.keras.version: ", tf.keras.__version__)
# print("tf.config.devices: ", tf.config.list_physical_devices())
# # Check that GPU is ... |
e728165e7b5526f21ee4950151986897d76e77d74f11eebef59e66fc2261202a | Python | 12,626 | 316 | """FIXD03-F12 regressions: the four D03-returned defects in the F12 lens
territory (browser-packet reserved prefix; evidence in the D03 themes packet).
- D03-R1: the transformer subject probe on a trace with a REUSED module
refuses ``lens_attention_subject_absent`` (factual absence of SUBJECT),
never the accessor'... |
efdcaafdbeddf570b2eb3e241b344329892ab7ba07ccee80a1c37408a40680c9 | Python | 12,627 | 356 | """Patching-helper honesty fixes (A03: WT1 A-I items 1 and 4; mikit F7/F8).
Three defect classes pinned here:
* attribution patching crashed on ANY model WITH parameters -- the
counterfactual guard's unconditional in-place restore bumped autograd
version counters of params consumed by the captured forwards (the w... |
b7b58ef56152079ed1214270371ca95eb1a004a16c69a26da295ac28bd4e265b | Python | 12,631 | 261 | #结论：当模型进行ensemble的时候性能会明显提升。
import json
import numpy as np
import os, sys
import random
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import to... |
493b74e6c50f5b6d08b92d3aa56c3a5699b7c72f3ca0da640f5685a506b23fc3 | Python | 12,636 | 305 | '''
PSNR methods check
author : obanmarcos
'''
import wandb
import torch
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as dlutils
f... |
c0702a83beb04e8a7fcfa009477d3c74ab8e94a8dfbbf916a04f69080f52bda6 | Python | 12,639 | 306 | '''
PSNR methods check
author : obanmarcos
'''
import wandb
import torch
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import pytorch_lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as d... |
b58cca18eea43b13861d68ea690936d345bc0e5415f5bf425e7067004e9c59ab | Python | 12,645 | 351 | # -*- coding: utf-8 -*-
from functools import partial
from itertools import repeat
import torch
from torchtext.data import Field, RawField
from bioseq2seq.constants import DefaultTokens
from bioseq2seq.inputters.datareader_base import DataReaderBase
from bioseq2seq.utils.misc import split_corpus
class TextDataReade... |
dbb7fe3daa31cf36b7f22e67979e9b4c860c73060ba730fdb7664b5f3a4264e5 | Python | 12,645 | 385 | #!/usr/bin/env python
#
# Copyright 2008, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
1f6c981cbad07fda6e06f454e83dba8a0ffa0b37622be43f09e6193a09619566 | Python | 12,655 | 276 | #
import time
import numpy as np
import torch
import torch.nn as nn
import torch.nn.modules.loss
import torch.nn.functional as F
from progress.bar import Bar
from sklearn.cluster import KMeans
from src.model import conST
from torch_geometric.utils import dropout_adj
from torch_sparse import SparseTensor
def drop_feat... |
b28033a9132ece5d811eda6f8e4eee30de5fad4960b04a717a5a939dad5f13f0 | Python | 12,659 | 405 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import sys
import argparse
import subprocess
import shlex
import logging
import re
import math
import glob
sys.path.insert(
0,
os.path.sep.join(
[os.path.dirname(os.pat... |
117330ce3e0a74d0774b9af5a359bb3204410e32645a84f8292c93588c9d2028 | Python | 12,666 | 238 | """
===========
Config file
===========
Configuration parameters for the study.
"""
import os
from socket import getfqdn
from fnames import FileNames
import pandas as pd
###############################################################################
# Determine which user is running the scripts on which machine and s... |
6521a4533bff9d450fc3d2d1353ce4eaed0618347a7230f98cc5c26c982f7c90 | Python | 12,666 | 349 | """F06: provocation rows for every attribution refusal code (S-17 coverage).
Every stable code the lane introduced ships PROVOKED (error-code coverage
gate): each test genuinely reaches its raise site and branches on
``exc.fields["code"]``, never message text. Codes provoked in the feature
suites are not duplicated he... |
7babe05581e89d7ee90561004a56076c5f6b92c855c812a1fdbb428cc8f76825 | Python | 12,669 | 373 | # Copyright (c) 2025, Wentao Guo, Ted Zadouri, Tri Dao.
import math
from typing import Optional, Type, Callable
import cutlass
import cutlass.cute as cute
from cutlass import Float32, Int32, const_expr
from cutlass.cute.nvgpu import cpasync
import cutlass.utils.blackwell_helpers as sm100_utils
from cutlass.cutlass_ds... |
4716a3193f3407c747ad123792d40c49ab95d4eb96b1204988dc77ccf01fb169 | Python | 12,673 | 237 | # !/usr/bin/env python
## created by Yun Hao @MooreLab 2021
## This script contains deep learning functions used in the DTox model construction
## Module
import sys
import numpy as np
import pandas as pd
import torch
from sklearn.metrics import roc_auc_score
from sklearn.metrics import balanced_accuracy_score
from sk... |
845cd452d4e1d4b4efb0e14710a5da7f8e00c4afc78ce206c75312118f7fe44a | Python | 12,676 | 302 | '''
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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... |
c219375b25e75f5fe09e84d0a4f3ad118d358e023534a32bb1c4e8cb1193cc8b | Python | 12,678 | 323 | """Regression tests for the per-draw collapse-rolling suffix memo.
Root cause (SPEEDENING wave 19): ``_collapsed_module_rolling_suffix`` is a pure
function of the captured graph, but the renderer re-entered it once per
collapsed-module NODE (``_render_nodes``, ``_render_dot``, ``render_ir``, and
``_single_op_module_sh... |
4c4a417bd438342738f90c424687448400620e06e9ab686860a59c634f161321 | Python | 12,679 | 352 | #!/usr/bin/env python
import argparse
import sys
import openbabel
from openbabel import pybel
openbabel.obErrorLog.StopLogging()
"""
Based on a script from TJ O'Donnell
https://gist.github.com/95387
Modified by B. Gruening and Hitesh Patel
Copyright 2009-2012 TJ O'Donnell, B.Gruening
"""
class Fragmenter:
def... |
2436687d4122a903536d142365f1ed391517d3d14c8d009e5c22bc4c47b33676 | Python | 12,680 | 285 | """
Tools to tailor a lookup table to a particular dataset.
Functions:
compute_splines: Computes the likelihood for a set of configs from a
precomputed lookup table.
"""
from __future__ import division
import numpy as np
from numba import njit
from pyrho.utility import get_table_idx, log_mult_coef
def ... |
3559e7a1012829b10f042cc3b4c5b8fe8bf471990dc98e27267d3a872a78077b | Python | 12,682 | 355 | import numpy as np
import pytorch_lightning as pl
import torch
from monai.networks.blocks import UnetOutBlock, UnetrBasicBlock,\
UnetrUpBlock, UnetrPrUpBlock
from monai.losses import DiceLoss
from survival_plus_x.models.vit import ViT3D
def proj_feat(x, hidden_size, feat_size):
"""
Reconvert the Attenti... |
2c1b045109ecaccc579b9464256a6cce8e04d7e8134b5e31f90927007e377946 | Python | 12,685 | 403 | import itertools
from mock import Mock, patch
import numpy as np
from numpy import testing as npt
from tns.astrocyte import space_colonization as tested
PCLOUD_POINTS = np.array([
[0.0, 0.0, 0.0],
[0.1, 0.1, 0.1],
[0.2, 0.2, 0.2],
[0.3, 0.3, 0.3],
[0.5, 0.5, 0.5],
[0.6, 0.6, 0.6]
])
def _po... |
5a4db9fd35c30f5280680f6af943e7528bda390a88b00de3ae4814b92a33ea50 | Python | 12,687 | 463 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
b553305532c96d694d6039bbaf5b8366fa035c166e78ee1692e97d3a052780b2 | Python | 12,691 | 292 | import os, qt, ctk, slicer, sys
import numpy as np
import vtk
from vtk.util.numpy_support import numpy_to_vtk
from SegmentEditorCommon.Helper import Helper
current_dir = os.path.dirname(os.path.abspath(__file__))
root_dir = os.path.abspath(os.path.join(current_dir, '..', '..', '..'))
sys.path.append(root_dir)
from bi... |
dc3b64b397cb71aa779127f9c4e3c0bae37d8da8857ae3c8d5c410e057425315 | Python | 12,692 | 344 | #!/usr/bin/env python3
"""
File: create_upsetplot.py
Created: 2021/05/10
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source ... |
50108c9eed7b34053cdd71b4ae79d39153832c77b848b60c90f3b379060f7ae5 | Python | 12,694 | 359 | """Generate the checked-in per-class StorageBinding tables.
One declared schema, generated artifacts (docs/reference/trace_core_design.md
section 3.4): this tool derives one ``StorageBinding`` per declared field for
all 12 record classes and writes ``torchlens/data_classes/_schema_bindings.py``
as reviewable, determin... |
60ee43675884fb0f7dee22b32f239b1ad08b8393c869e0e9bc7767d6a3fdba7f | Python | 12,700 | 317 | ##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
## This file is par... |
e1ef7c2cfe77fcb8e61b14c98d1bded060b50caea5ceda5efb3cda4067815398 | Python | 12,701 | 378 | #!/usr/bin/env python
#
# Copyright 2009 Google Inc. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
82b61d30f62d6eddd81ff63b43146fd4f7be93be767ae5561b74a99951c24eca | Python | 12,703 | 387 | """Hierarchy of format OME-Zarr implementations."""
import logging
from abc import ABC, abstractmethod
from collections.abc import Iterator, Mapping
from typing import Any
from zarr.storage import FsspecStore, LocalStore
LOGGER = logging.getLogger("ome_zarr.format")
def format_from_version(version: str) -> "Format... |
3259e972cdf8892137a5b4bb92e8f215952e96000e14ae96e590ca0c2986db21 | Python | 12,706 | 343 | """
ComposedStimulator — configurable trigger + action stimulator.
Replaces the flat list of monolithic stimulator classes with a two-step
selection model: users choose a trigger condition (WHEN to stimulate) and
a stimulus action (WHAT to deliver), and this class wires them together.
All mAGO-based hardware uses the... |
9d024b142daba63b3210ba692263a6a22990a9995c120641cdf65c0c8d711483 | Python | 12,710 | 289 | """
Manager and Serializers for Quotas.
For more information about quotas: https://galaxyproject.org/admin/disk-quotas/
"""
import logging
from typing import (
cast,
)
from sqlalchemy import (
and_,
select,
)
from galaxy import (
model,
util,
)
from galaxy.exceptions import ActionInputError
from... |
32309cf72d01f76a7a853578454a356fe6658561bda8d60155a41bf329aac76d | Python | 12,712 | 348 | from __future__ import annotations
import argparse
from pathlib import Path
import numpy as np
import pandas as pd
from autotransop import (
AdversaryConfig,
AutoTransOP,
AutoTransOPConfig,
AutoTransOPTrainer,
DomainConfig,
DomainEffectConfig,
DomainTensorData,
HeadConfig,
MLPConf... |
556748a3ee5ccb5deccbacf4a825b5a79bf42441815e7d86a1a63e90a8eeb28e | Python | 12,714 | 355 | import os
import platform
#The API is not snake case which triggers linter errors
#pylint: disable=invalid-name
if platform.system().lower() == "windows":
dslib_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'lib')
# On Windows, we can't rely on RPATH being set to $ORIGIN/lib/ or on
# @... |
85f0e7e86c9c775cb6d15e1088b3609a3e3833b80d3f00d67864e774c1d78457 | Python | 12,716 | 301 | """
08: Fitting Groups of Spectra
=============================
Using the group model object to run fit models across multiple power spectra.
"""
###################################################################################################
# Import the group model object
from specparam import SpectralGroupMode... |
24e4c5356afbed9c4a50a8f0f1349b37ed9d93ee98c26a8dd8e72b36487b2557 | Python | 12,717 | 250 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""tests for parse.py"""
import unittest
from os import remove
import numpy as np
from sknetwork.data import parse
class TestParser(unittest.TestCase):
def test_unlabeled_unweighted(self):
self.stub_data_1 = 'stub_1.txt'
with open(self.stub_data_1... |
8d33f6f04390948e51d9521f26766fdf45a98862387d3a13c85f9b6becbe48e2 | Python | 12,720 | 293 | """Round-36 security regression: module-less tensor-method smuggling under trust.
r35 fixed the ``__module__``-missing / ``or <trusted-module>`` fallback loophole on
the intervention resolver's **torchlens-walk** foreign branch (by routing the
resolved object through ``is_pure_forward_callable`` on its REAL identity).... |
507827d396a869afc86462b8fbfc33f6a0ea15dd00df26224883b940fa23c2e8 | Python | 12,726 | 309 | """Plots for annotating power spectrum fittings and models."""
import numpy as np
from specparam.utils.select import nearest_ind
from specparam.data.periodic import get_band_peak, sort_peaks
from specparam.params.periodic import compute_fwhm
from specparam.params.aperiodic import compute_knee_frequency
from specparam... |
cc83f694defda0960305fc2c309bac3209abb89b60d25da562f89d2b05bc0109 | Python | 12,728 | 305 | from keras.src import activations
from keras.src import constraints
from keras.src import initializers
from keras.src import ops
from keras.src import regularizers
from keras.src.api_export import keras_export
from keras.src.layers.input_spec import InputSpec
from keras.src.layers.layer import Layer
from keras.src.quan... |
d5e61bd1df2a968ac2101de28861e266e3489b1de1bc1c8f7f10beacc44c7113 | Python | 12,728 | 272 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import types
from pathlib import Path
from typing import Any
import torch
from torch import nn
from ultralytics.nn.modules import Detect
from ultralytics.utils import LOGGER
from ultralytics.utils.checks import ch... |
a6eae94d6ac50e7d9b757913a8d422f8dd8e045ba5cee6dcf60af5f6e5007f67 | Python | 12,732 | 338 | """Implementation of a space that represents closed boxes in euclidean space."""
from typing import Dict, List, Optional, Sequence, SupportsFloat, Tuple, Type, Union
import numpy as np
import gym.error
from gym import logger
from gym.spaces.space import Space
def _short_repr(arr: np.ndarray) -> str:
"""Create a... |
b248db533d796d6f638b047a5b74fe90ab7bdc21a32492baf9a54fd451330e4e | Python | 12,739 | 307 | import torch
import torch.nn as nn
import torch.nn.functional as F
from opt_einsum import contract as einsum
import torch.utils.checkpoint as checkpoint
from util import get_tips
from util_module import Dropout, create_custom_forward, rbf, init_lecun_normal
from Attention_module import Attention, FeedForwardLayer, Atte... |
3b55d1fa5f2505c2ad705e37d4edd7a88fbf9356465a16054072ebbee912b83d | Python | 12,740 | 360 | import numpy as np
from utils import Q_nak
from mitosfns import spike_quanta, run_sim
from steady_state import get_steady_state
from gates import ros_inf
import figure_properties as fp
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib import patches
from matplotlib.ticker import F... |
881ed5c68cef7789c5f5c3b1c23b0af4635a45e4b66ae78a547d363fed299f01 | Python | 12,740 | 385 | """Internal worker state (global).
This includes the currently active and reserved tasks,
statistics, and revoked tasks.
"""
import os
import platform
import shelve
import sys
import weakref
import zlib
from collections import Counter
from kombu.serialization import pickle, pickle_protocol
from kombu.utils.objects im... |
2db89488ff38475b8ec933770db167f6f19f0a5bfba8bbc566b46206859d6f5b | Python | 12,743 | 375 | """Shared code for working with workbook data.
Module was developed for sample sheet work but extracted for reuse with fetch
workbooks.
"""
import base64
from collections.abc import Generator
from csv import (
Dialect,
reader,
Sniffer,
)
from dataclasses import dataclass
from io import (
BytesIO,
... |
7a4fba082453eb87a7b5535204e5b5aec6830bebd6141199ec723ea6a446587d | Python | 12,746 | 358 | """Google Cloud Storage result store backend for Celery."""
from concurrent.futures import ThreadPoolExecutor
from datetime import datetime, timedelta, timezone
from os import getpid
from threading import RLock
from kombu.utils.encoding import bytes_to_str
from kombu.utils.functional import dictfilter
from kombu.utils... |
b9a4c0bae77453c7b191eb73b6f052edaea308e312901689f4940364a0c62ba5 | Python | 12,755 | 288 | """
calibration.py — per-microphone UMIK-1 SPL calibration.
Every miniDSP UMIK-1 ships with a unique, factory-measured frequency-
response correction curve (and an overall "Sens Factor" offset) keyed to
that specific physical unit's serial number. This module parses that file
and applies it to compute a calibrated, pe... |
64e9ef591979ad553f96bcc71a6756193b559871c218ea9a80305e9b99d473a9 | Python | 12,756 | 351 | """Tangent space functions."""
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from .utils.utils import check_version
from .utils.mean import mean_covariance
from .utils.tangentspace import tangent_space, untangent_space
if check_version('sklearn', '0.17'):
from sklearn.discriminant_an... |
273a85559cb2aa97c83cd9fd0058415ee43194c72adfa0c2ff56729bc32ef5dd | Python | 12,758 | 318 | # Python
from timeit import default_timer as timer
# 3rd party
import torch
# NITorch
from nitorch.spatial import (affine_grid, grid_pull, voxel_size)
from nitorch.core.optim import (get_gain, plot_convergence)
from nitorch.plot.volumes import show_slices
from nitorch.core._linalg_expm import _expm
# UniRes
from ._proj... |
719235b7b283b3f252e3535671b09c06db570c2d326cf2bb9a1d55a665038e13 | Python | 12,758 | 319 | #!/usr/bin/env python3
"""
Dx Z+++ — test two candidate fixes for the brainlat noise problem.
c1: Drop the 4 most-distorted features (fooof_off, fooof_exp, dfa,
a_asym_front) from the canonical 15-feature pool. Re-run with all
4 AD cohorts. If those features were the noise source, including
brainlat should... |
b64caaa1df2d287916933ba0cef0a0cdd91e1027b730bff355e2998d3538fed8 | Python | 12,761 | 362 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
02eee5c6940aeec995242c735305e88dee8a94eb8a9e1be45ac81817931cef90 | Python | 12,762 | 370 | import os
import sys
from typing import Any, Dict, Generic, List, Literal, Optional, Type, Union, cast
import dask.array as da
import dask_ml as dml
import numpy as np
import seqpro as sp
import xarray as xr
from sklearn.preprocessing import StandardScaler
bin_dir = os.path.dirname(sys.executable)
os.environ["PATH"] ... |
ae4c41f93bf3330714c4dcde55df7e3a9a1174381a96f714d45a35804015ca01 | Python | 12,763 | 411 | # SOURCE: vendored from clovaai/ext_portrait_segmentation @ master
# https://raw.githubusercontent.com/clovaai/ext_portrait_segmentation/master/models/SINet.py
#
# Park, Hong, Roh, Ha, Han 2020 "SINet: Extreme Lightweight Portrait Segmentation
# Networks with Spatial Squeeze Module and Information Blocking Decoder" (WA... |
c5ec8d541646763747571f3aac7942162bdd5a98b458109ea340b16b4ac6f74f | Python | 12,767 | 359 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Button(_BaseLayoutHierarchyType):
_parent_path_str = "layout.updatemenu"
... |
5029869f5146ff8ebba5ffab9604a1a629622f584f39090282fb3546ae0ea078 | Python | 12,769 | 332 | #!/usr/bin/env python3
"""
Diagnostic S — incremental evaluation of three new feature families.
Features added to the Dx P canonical pool:
- Sub-alpha: 8-10 Hz vs 10-12 Hz band powers + ratio (global + posterior)
- DMN-proxy connectivity: midline (Fz-Pz) and lateral (F3-P7 / F4-P8)
iPLV and dPLI in alpha and t... |
9d8f8e6753be79455b7ab2f6d9a4b6a653b7f17b1e6e82affdbee398d79a6b1c | Python | 12,769 | 299 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
799479ed4d610de21d953e27e39d253e0108bca2da9005bb1e0e71b34b461206 | Python | 12,771 | 264 | import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torch.utils.dat... |
e3eb3392422d2d44deedbca9591d001e975dd713da4ab420226fdf5fb1c328e0 | Python | 12,772 | 321 | '''
PSNR methods check
author : obanmarcos
'''
from cgi import test
import wandb
import torch
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_u... |
d8f1ce380158cd993a0632ec494b35b50c02d911068593fceb140a216f791f67 | Python | 12,775 | 267 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
4be583ffae6f8490533ee118d178e8dc5a2d98f6f626c9ce95a205d892d3d8b3 | Python | 12,776 | 323 | '''
PSNR methods check
author : obanmarcos
'''
from cgi import test
import wandb
import torch
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import pytorch_lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import datal... |
82f32047a936bffa127c897bdac5a0114099c28df6f502ab53bed35d0e137157 | Python | 12,779 | 351 | """L3 trailing-lane gates for detachable CUDA kernel telemetry."""
from __future__ import annotations
import ast
import importlib
import re
from pathlib import Path
import pytest
import torch
from _source_corpus import module_ast
from torch import nn
import torchlens as tl
from torchlens import kernel_telemetry as ... |
43cdec3993d4122404bc070c1715a16d512ecff282f3739210b232f274990137 | Python | 12,780 | 364 | """Preview-backend teardown contract: guaranteed cleanup + settle-after-cleanup.
R17-1/R50-1 (b5 parity lane): MLX and Paddle previously stamped COMPLETE/HALTED
inside the capture ``try`` and ran fallible teardown in ``finally`` -- a
teardown raise propagated with the stamp intact, and a raising session cleanup
skippe... |
3556b81c0b617a1e91098c1ecf825de9de79c8751b62f66d11df7be7786c986d | Python | 12,782 | 362 | # SOURCE: vendored from https://github.com/awslabs/gluonts (PR #1617, "Adding NCAD
# (Neural Contextual Anomaly Detection for Time Series) to nursery")
# @ 396192e17e99a881a9b95229f9ff11ad2e685008
# (src/gluonts/nursery/ncad/src/ncad/model/tcn_encoder.py::Chomp1d/TCNBlock/TCN/
# TCNEncoder + contrastive_clasifier.py::... |
adbe35f2be6afd5c12a35ac4953c84c9b173a321fdf491ee51b3e33361b5471e | Python | 12,782 | 274 | import csv
import hashlib
import json
import unittest
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
def read_normalized_markdown(relative):
return " ".join((ROOT / relative).read_text().split())
class RepositoryContractTest(unittest.TestCase):
ASSET_HASHES = {
"src/models/sta... |
3e29115bd8150dab935607df26acb5a190d9101d67dd59cc71a6d30e1f46830b | Python | 12,785 | 484 | #!/usr/bin/env python3
import os
import sys
import numpy as np
from htmd.ui import *
from moleculekit.tools.voxeldescriptors import getVoxelDescriptors,getCenters, rotateCoordinates
from moleculekit.tools.atomtyper import prepareProteinForAtomtyping
from Bio.PDB import PDBParser, NeighborSearch
import subprocess
impor... |
a32c36fd3eabe5924c7ad473d22cd012bd84872ad686092ac3689d83ab7672b8 | Python | 12,787 | 278 | """P1-9 · MDC95 的层级纠正：个体层阈值 vs 组均值层阈值。
为什么这个脚本必须存在
----------------------
稿件 3.9(a) 的核心论断是"没有任何位移越过它自己的噪声底"，论据是
肺时钟位移 2.17 clock units vs 自身 MDC95 3.78 → 比值 0.57（未达）
这个比较**把两个不同层级的量放在了一起**。MDC95 = 1.96·√2·SD_within 是
**个体**层面的最小可检出变化 —— 它回答"同一个人两次测量要差多少才算真变了"。
而 2.17 是**九个人的组均值**位移。组均值的噪声底不是 SD_within，而是它的
标... |
fa166ada7d0016dfc95f3a6186e519dd7ce35ffebf566db455554889920b02d6 | Python | 12,788 | 303 | from src.cfg import *
def load_useful_variables(data_repository):
data_repository = os.path.abspath(data_repository)
try:
with open(os.path.join(data_repository, 'ccf3_acr2id.json')) as fp:
acr2id = json.load(fp)
with open(os.path.join(data_repository,'ancestorsById.j... |
14935bc367f16d37cd343edf711ba1f22a403a1c514b263ccbe8026f52df5825 | Python | 12,791 | 365 | import pickle
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from pytest import approx
from sklearn.dummy import DummyClassifier
from conftest import get_distances, get_means, get_metrics
from pyriemann.estimation import Covariances
from pyriemann.utils.kernel import kernel
from pyriema... |
3d0175cee68a360981bb4a66d67950663bbd51c89a982cedc2847ffa73346836 | Python | 12,793 | 315 | """A05 escrow-spill fix: the four-panel red tests (leverage B2, brainpipe 2,
transforms P7, tvscope B13).
Root cause (review T3, conceded 3-0): deferred final-numbering selectors (op
labels, positive ordinals, ``output``) escrow every candidate payload and
spill past the 64 MiB RAM budget via ``torch.save``; a capture... |
88e5863d9fe1da0e4a461ffebf237372e2471aced5485c3a6cb0d65142659c88 | Python | 12,799 | 404 | """
Utility Routines for Working with Matplotlib Objects
====================================================
"""
import itertools
import io
import base64
import numpy as np
import warnings
import matplotlib
from matplotlib.colors import colorConverter
from matplotlib.path import Path
from matplotlib.markers import... |
81cdd0a18aa42555b865a479c7fb4775bad9f9f8724ec23adc9862a989a94b14 | Python | 12,802 | 473 | """
https://fastapi.tiangolo.com/tutorial/sql-databases/
To avoid confusion between the SQLAlchemy models and the Pydantic models, we will have the file models.py with the SQLAlchemy models, and the file schemas.py with the Pydantic models.
These Pydantic models define more or less a "schema" (a valid data shape).
S... |
38091a29852252ed13f2cf26391d8d90c8e25dad42b9d099d20ab59998e645ef | Python | 12,805 | 336 | """Static FIELD_ORDER / FieldPolicy / portable-state contract tests."""
from __future__ import annotations
from collections.abc import Collection
from dataclasses import dataclass
from typing import Any
from torchlens import constants
from torchlens._io import FieldPolicy
from torchlens.data_classes.buffer import Bu... |
9f3106395760917406dca9e86f715a60a0b47095d8bf67b755b218006d2639dc | Python | 12,805 | 429 | # -*- coding: utf-8 -*-
#
# Time-frequency analysis with superlets
# Based on 'Time-frequency super-resolution with superlets'
# by Moca et al., 2021 Nature Communications
#
# Implementation by Gregor Mönke: github.com/tensionhead
#
import numpy as np
from scipy.signal import fftconvolve
def superlet(
data_arr,... |
f8302a2256f1a88628119ed19ea44f8b34773366478d101ee405d4295bd21c22 | Python | 12,810 | 264 | import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torch.utils.dat... |
94a091eeb19ef2ee2833577224720a2f64043387b6df4dc976fc97b05400cc08 | Python | 12,813 | 265 | #结论：当模型进行ensemble的时候性能会明显提升。
import json
import numpy as np
import os, sys
import random
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import to... |
91756b3e16318c2023eca21ffbf44a22bb788b1270a1a2b0c01b0c508f8c07a7 | Python | 12,815 | 303 | """Manager and Serializer for library datasets."""
import logging
from typing import (
Any,
)
from sqlalchemy import select
from galaxy import util
from galaxy.exceptions import (
InsufficientPermissionsException,
InternalServerError,
ObjectNotFound,
RequestParameterInvalidException,
)
from galax... |
9ebe3b4e86bc7be492f7ed89507f0921317da82678e5aeec3aac1c0aabba693d | Python | 12,820 | 289 | """tviz real-model corpus rows (tviz memo section 7, R1-R6).
All rows run offline against locally cached checkpoints, eval mode, fixed
prompts. The headline acceptance test is R1-vs-R2: the eager OBSERVED
pattern and the SDPA RECONSTRUCTED pattern come from the same weights and
must agree within dtype tolerance, each ... |
ea33ea4d3dee4703751288e5145fc8be54ec99f6c57e8de2c8dcc32d3312a597 | Python | 12,825 | 344 | import os
import numpy as np
import json
import h5py
import random
import pandas as pd
import tensorflow as tf
binary_ce = tf.keras.losses.BinaryCrossentropy()
binary_acc = tf.keras.metrics.BinaryAccuracy()
categorical_ce = tf.keras.metrics.CategoricalCrossentropy(from_logits=True)
def read_saved_file(file_path):
... |
7d218445047f89fd863777ce4ca72c864824908d0cd3b18a150a6cd12a0f13d6 | Python | 12,826 | 308 | """
Author: Derek van Tilborg -- TU/e -- June 2022
Inspired by:
Moret, M., Grisoni, F., Katzberger, P. & Schneider, G.
Perplexity-based molecule ranking and bias estimation of chemical language models.
ChemRxiv (2021) doi:10.26434/chemrxiv-2021-zv6f1-v2.
- LSTM: LSTM model class
-... |
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