sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
96079cf8b702df29aba6a3b1d20c0ec9a93791d2b6b70da22e2a56b2106e76b8 | Python | 7,708 | 202 | from keras.src import backend
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.callbacks.callback import Callback
@keras_export("keras.callbacks.SwapEMAWeights")
class SwapEMAWeights(Callback):
"""Swaps model weights and EMA weights before and after evaluation.
This call... |
c60434eea2c509ee2a2e076d58f00f3e04cd14347041c399ee7482a1a3f60373 | Python | 7,708 | 283 | """Read-compatibility tests for TorchLens 2.16.0 ``.tlspec`` fixtures."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.intervention.types import HelperSpec, InterventionSpec
from torchlens.opt... |
6d16ff4bcd3f19c874f9e02d35f972400b2611e48540415f3d1bf17072a7f249 | Python | 7,709 | 229 | # Copyright 2022 Deepfold 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... |
ed4df050d73b4e5823f9ca6e460b516d7cef4c73cbdba2d8b20eb7379be5b000 | Python | 7,709 | 230 | """Tests for the specparam.models.event, including the event model object and it's methods.
NOTES
-----
The tests here are not strong tests for accuracy.
They serve rather as 'smoke tests', for if anything fails completely.
"""
import numpy as np
from specparam.models import SpectralGroupModel, SpectralTimeModel
fro... |
f56471b3feccfba0e3906f79b67754abe662359b83bf4fda44b85fa2cf201584 | Python | 7,709 | 211 | # coding=utf-8
# Copyright 2023 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... |
bed1f9bfb38715224cbbafa5fbe93ed832dc0a88989fb332074ad2621df391de | Python | 7,713 | 237 | """
module for custom functions used for creating and training the model
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision
import torchvision.models
import pytorch_lightning as pl
from time import time
import scipy
from pytorch_lightning.utilities.types import EVAL_DATALOADERS, ... |
ba1392c85dde67bbf672cef0a7bac9e1ece355e04778cd1456247f6189f968dd | Python | 7,715 | 208 | from collections import namedtuple
import os
import struct
from time import sleep
import nibabel as nb
import numpy as np
import string
def mosaic(data):
x, y, z = data.shape
n = np.ceil(np.sqrt(z))
X = np.zeros((n*x, n*y), dtype=data.dtype)
for idx in range(z):
x_idx = int(np.floor(idx/n)) * ... |
6a390018e016ce5e6a2465f4c906b438ad98c4a4ee361c8e74ed2ce48bc7fd64 | Python | 7,716 | 212 | """Tinygrad recurrence grouping: multi-pass layers, relabel safety, tamper oracles."""
from __future__ import annotations
import dataclasses
from typing import Any
import pytest
tinygrad = pytest.importorskip("tinygrad")
from tinygrad import Tensor # noqa: E402
import torchlens as tl # noqa: E402
from torchlens... |
afa54990e4aedc14abd55fd9fac93fcb3a5c0b0364dccba9d7c8235f592ae471 | Python | 7,716 | 208 | #!/usr/bin/env python3
"""
File: create_replication_heatmap.py
Created: 2022/12/20
Last Changed:
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 t... |
f184235168d45fd79acc7ba1a9d17e30fc919beb1b5509bedc20d613c88b4b8e | Python | 7,716 | 171 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Do very simple cleaning of .bam files for ATAC-seq data pre-processing.
#
# This script:
# * Drops low mapping quality reads (<10)
# * Removes chrM mitochondrial reads
# * Removes PCR duplicates (using samtools)
# * Removes blacklisted regions (from ENCODE or custom bla... |
d3654ce822050bac94952fc4ce8191693aec8ee1f96652735bdb6ccaa7a430e1 | Python | 7,720 | 154 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
688bb5fb2e4a10dad5eb23b0eae4da0c7647c00f7f1b56b1abcf64b356050f28 | Python | 7,722 | 244 | import tensorflow as tf
from tensorflow import keras
from functools import partial
import numpy as np
import os
import cv2
from tensorflow.keras.preprocessing.image import ImageDataGenerator
def crop_top(img, percent=0.15):
offset = int(img.shape[0] * percent)
return img[offset:]
def central_crop(img):
... |
965f96369cc0e5b5001e7fc5d0a2c878f9b7a7e5dafbf796b88ae39d04156ff8 | Python | 7,723 | 197 | #!/usr/bin/env python3
"""
Dx Y2 — severity-stratified sensitivity under the Dx AA canonical tool.
Re-runs Dx Y but applies the rank-norm + whitening + Quad_LDA pipeline
that became canonical at Dx AA, instead of the z-score tool that Dx Y
originally used.
Same severity bands as Dx Y:
- Severe: MMSE < 12 (or MoCA ≤ 1... |
a22554be91150277ffc9220d8dc9355170cea45a8a1b7eced14aacf84fdcc273 | Python | 7,723 | 207 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Data loader."""
import itertools
from functools import partial
import numpy as np
import torch
from slowfast.datasets.multigrid_helper import ShortCycleBatchSampler
from torch.utils.data._utils.collate import default_co... |
2f7e8e7b2e44dcfca64e39202a2254aa3245d7ee686ac38b9d919df0dad6bbc5 | Python | 7,724 | 195 | from typing import Iterable, List, Optional
from codecarbon.core import gpu_amd, gpu_nvidia
from codecarbon.core.gpu_device import GPUDevice
from codecarbon.core.units import Time
from codecarbon.external.logger import logger
AMDSMI_AVAILABLE = gpu_amd.AMDSMI_AVAILABLE
PYNVML_AVAILABLE = gpu_nvidia.PYNVML_AVAILABLE
... |
65229e75e5238f1c65d97ee3ca32d36e630859ce876c01ba190778cfe862d829 | Python | 7,724 | 218 | import numpy as np
import scipy.stats
from ridge_utils.npp import mcorr
def model_pvalue(wts, stim, resp, nboot=1e4, randinds=None):
"""Computes a bootstrap p-value by resampling the [wts] of the model, which
is [wts] * [stim] ~ [resp].
"""
origcorr = np.corrcoef(resp, np.dot(stim, wts))[0,1]
if ra... |
ac562a832e4a749a6a899fa7fb8108d88122cfe23151081b598417b6acb8d4a9 | Python | 7,724 | 201 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test objects and function in tfep.nn.transformers.mixed.
"""
# ===============================================... |
d6973bba3cc9bde1b224fc629f38177b0bdb47f5d440b2dd10cfe4f36c87cd22 | Python | 7,724 | 176 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Depth estimation trainer for YOLO models."""
from __future__ import annotations
from copy import copy
from pathlib import Path
from typing import Any
import torch
from ultralytics.models import yolo
from ultralytics.models.yolo.detect import Det... |
16ee3051d550b5f3e530b734480ddcddba6542333ab164bd70d67708b7ea2d52 | Python | 7,726 | 239 | """Tests for Phase 6 NaN/Inf debugging affordances."""
from __future__ import annotations
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.errors import CaptureError
from torchlens.partial import PartialTrace
class NonFiniteFixture(nn.Module):
"""Tiny module that produces N... |
e2beecdcf7807be6246eed5b3a878d851f6d705309d40b5331a9cf0d2d31b8ec | Python | 7,728 | 183 | """
Functions for parsing and verifying input parameters.
Copyright (C) 2021 Tham Cheng Yong
This file is part of NanoVar.
NanoVar is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License... |
c65fc5de672039d30a743dcb9f79b3c6ca2adec51221491cf674d770a6327f9d | Python | 7,731 | 259 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Lighting(_BaseTraceHierarchyType):
_parent_path_str = "cone"
_path_str = ... |
15f7dcb8f169764f9f83ee173cc818502b60e15b1bc0babfbcb0b8df66b1d058 | Python | 7,733 | 241 | """
Model architecture from open_ipcl repository.
https://github.com/harvard-visionlab/open_ipcl
MIT License
Copyright (c) 2021 grez72
## Architecture modified by jfeather for metamer code compatability##
"""
from __future__ import print_function
import torch
import torch.nn as nn
from IPython.core.debugger import... |
a7bda7e149ad09d46bfe18ab2a5dbfc72cafa1ec080a2a3f54f0ad8c24de862f | Python | 7,733 | 219 | # Copyright 2022 Deepfold 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... |
afb93777d32a5972653e41d842e82a3aeee03ee4d4c3114a140ee813c8427978 | Python | 7,733 | 163 | from __future__ import print_function
import tensorflow as tf
import os, argparse, pathlib
from eval import eval
from data import BalanceCovidDataset
# To remove TF Warnings
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
parser = argparse.ArgumentParser(descri... |
a62e45c5eb28ef1f028252032defec3b5b3fa82944cd4880d10abdcc1bd0c048 | Python | 7,737 | 234 | import os
import cv2
import numpy as np
import scipy.ndimage
from torch.nn.functional import cosine_similarity
import torch
from matplotlib import pyplot as plt
def denormalize_(image): # 去归一化
image = image * (255 - 0) + 0
return image
def array2image(array):
image = np.ceil(255 * (a... |
7f8780e7e62943d02b3a6ba67165e0a17928374b39ba3d0c9b017cecab853e5f | Python | 7,738 | 201 | import lzma
import zlib
import pytest
DATA = b"pyrosm reads OpenStreetMap data " * 64
@pytest.mark.parametrize(
"case, stream, size, expected",
[
("declared size", zlib.compress(DATA), len(DATA), DATA),
("size too small", zlib.compress(DATA), len(DATA) - 1, None),
("size too large",... |
da3a9dd1b85489872b07752d234ddae56f8852f7efd7cfcfd4765f02d38540e5 | Python | 7,738 | 196 | import warnings
from typing import Any
import gymnasium as gym
import numpy as np
import pytest
from matplotlib import pyplot as plt
import neurogym as ngym
from neurogym import _PSYCHOPY_INSTALLED
from neurogym.core import BaseEnv, TrialEnv
from neurogym.envs.registration import all_envs, all_tags, make
from neurogy... |
eff1cdc4049549ef2e7cc5fe8fa75e9704339adaf91a9881b553d51947bd4e3e | Python | 7,738 | 188 | import os
import random
import numpy as np
import json
from collections import OrderedDict
def seq_format(proteins_dic, output_dir):
# datasets = ['kiba', 'davis']
# for dataset in datasets:
# seq_path = os.path.join('data', dataset, 'seq_original')
# fpath = os.path.join('data', dataset, 'proteins.tx... |
aff01421aea0d3dc7d09e29ce140582b80c47bc43506abccb351be8c2e425dba | Python | 7,739 | 268 | """P1 backward sidecar trigger and registry tests."""
from __future__ import annotations
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.backends.torch import backward as backward_mod
from torchlens.backends.torch.backward import (
_BACKWARD_GRAD_FN_R... |
f10908cd68e35d023c50897aecf72becd509e6f6fb149db51531206e292f1073 | Python | 7,739 | 185 | """Smoke-tier wiring test for ``benchmarks/perf_gate.py`` (b10 R78 round-3).
The perf gate existed with NO smoke-tier exercise: a refactor could break its
import, its baseline files, or its comparison math and nothing red would show
until someone ran a real benchmark. This file imports the gate machinery,
checks the c... |
f31e6fa3d182114c9e4223dd6eb65a0808d8ecd42f9a3f37342b0aac0c1f1bba | Python | 7,742 | 203 | """Phase 2 capture-unification regression tests."""
from __future__ import annotations
import inspect
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens import _state
from torchlens.backends._protocol import CaptureBackend
from torch... |
7555afd10a47c8b568a18edd648ed64b17460d9ee9734f16c943919925ca5e5b | Python | 7,744 | 229 | ### Support for some raw binary data formats (MLF, PLS, PIC)
### MLF is format by Moor Instruments
### PLS is format by D. Postnov (jr)
### PIC format is used on CCDB
import numpy as np
from numpy import uint16, uint32, uint64
from numpy import int16, int32, int64
import numbers
def read_at(fid, pos, Nelem=1, dtype=u... |
e6d95d4047859027e23b654761867a8b214cdc98fd486ec9d3683e43f22c9021 | Python | 7,746 | 210 | import os
import pandas as pd
from PIL import Image
import torch
from hn_cnn.constants import *
from hn_cnn.image_preprocessing import process_scan
# Mapping for the clinical data
# Include each variable: Primary Site, T-stage, N-stage, ...
# Key: the name of the column containing the variable in the dataset
# ... |
8f4ae879fc5d269176cfe9eb5104b27a2952f0cca32948532933b7784d990141 | Python | 7,747 | 258 |
import numpy as np
import matplotlib.backends.backend_pdf
import matplotlib.pyplot as plt
from analysis_utils import get_adjacency
plt.rcParams['figure.figsize'] = (5, 5)
plt.rcParams.update({'font.size': 20})
freq = ['0.015_0.75_pinknoise.mp4',
'0.015_1.5_pinknoise.mp4',
'0.015_12_pinknoise.mp4',
'0.015_3... |
a56f353b14104d6402b5edfc025fae5446b732d5d632c9a799b8eef1db70b259 | Python | 7,752 | 193 | """ Translation main class """
import os
import torch
from bioseq2seq.constants import DefaultTokens
from bioseq2seq.inputters.text_dataset import TextMultiField
from bioseq2seq.utils.alignment import build_align_pharaoh
import seaborn as sns
import matplotlib.pyplot as plt
class TranslationBuilder(object):
"""
... |
0c6dd5cda69d9586848806befaf7cc684113f68a8fe72adcab3db98c0b510fa1 | Python | 7,753 | 175 | import numpy as np
import vtk, slicer
import vtk.util.numpy_support as vtk_np
from slicer import vtkMRMLScalarVolumeNode
from slicer import vtkMRMLLabelMapVolumeNode
from biomedisa_extension.SegmentEditorBiomedisaPrediction.Logic.BiomedisaPredictionParameter import BiomedisaPredictionParameter
from biomedisa_extension.... |
4ebaf0545e9db4a0e75f5f7845decb1adc457b76254f5a7ec1819c926ba5a639 | Python | 7,753 | 260 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Lighting(_BaseTraceHierarchyType):
_parent_path_str = "mesh3d"
_path_str ... |
d33a38d992e01302c01c4eb70b30647b40e113eaeabb269f09bc951e6afcbdf7 | Python | 7,753 | 260 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Lighting(_BaseTraceHierarchyType):
_parent_path_str = "volume"
_path_str ... |
3ca218cd35bb1dba5c08c1733f025e6e27c65a25e2e2e718a23cdc6541140b6d | Python | 7,754 | 205 | import os
import numpy as np
import pandas as pd
from mirp.settings.generic import SettingsClass
from mirp.settings.transformation_parameters import ImageTransformationSettingsClass
from mirp.settings.feature_parameters import FeatureExtractionSettingsClass
from mirp.settings.resegmentation_parameters import Resegmen... |
552f128ebdc87809e774ea648c2e8c13e40b140ec2e9f7068a7c75f9cbcc3fa2 | Python | 7,757 | 205 | try:
import llspy
except ImportError:
import os
import sys
thisDirectory = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(thisDirectory, os.pardir, os.pardir))
import llspy
import json
import multiprocessing
import os
import sys
import time
from distutils.version impor... |
636c3eae5daabfb28facf8366c3d917f6a1bc10061d1caa06459a85e06fd07fd | Python | 7,757 | 219 | # coding=utf-8
# Copyright 2024 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... |
cc0a5a95652207250e117ffe515c061c66d352f8fc007dfc332a1b48c0155501 | Python | 7,757 | 259 | """
Plot previous choice weights against previous stimulus weights
"""
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pylab as pl
import seaborn as sns
import pycircstat as pc
matplotlib.rcParams["pdf.fonttype"] = 42
sns.set(
style="ticks",
font="Helvetica",
... |
0ee509ccb0a314940b477cc9a627fd43f76448d6cf4449cc4f0d6e3cec21134d | Python | 7,760 | 215 | """Robustness sprint PR 3 — parallel/framework robustness.
Covers the parallel-wrapper and framework-integration subset of the catalog:
- ``DistributedDataParallel`` unwraps via ``.module`` just like ``DataParallel``
(previously only the latter was handled, so DDP users got silently-wrong
layer addres... |
363beb9b876bbf31b95f777aad7029eb3c62776ac19c8ab20010de90b78a15b1 | Python | 7,760 | 220 | import os
from tqdm import tqdm
import os.path as osp
from typing import *
from torch_geometric.data import (
Data,
InMemoryDataset,
download_url,
extract_zip,
)
import numpy as np
import torch
from torch import Tensor
from torch_geometric.utils import scatter
from torch_geometric.data import Data, ... |
952fad85f359800a42d1b9e5cde7f1e968ec260592a4c7dfcf408852f0a55f43 | Python | 7,760 | 226 | from argparse import ArgumentParser
from typing import Any
import torch
from pytorch_lightning import LightningModule, Trainer, seed_everything
from torch import Tensor, nn
from torch.utils.data import DataLoader
from pl_bolts.callbacks import LatentDimInterpolator, TensorboardGenerativeModelImageSampler
from pl_bolt... |
0c5c88b0fa72138efd785447da81812f5eeb1c16dbab925cb807790ed82df69f | Python | 7,761 | 171 | """Place cell related functions."""
import numpy as np
from spiketools.spatial.utils import compute_nbins
from spiketools.spatial.occupancy import compute_bin_counts_pos
from spiketools.spatial.checks import check_bin_definition
from spiketools.utils.checks import check_array_orientation
from spiketools.utils.extract... |
c4f74f5fbdaec651b5638bc86892bc73a2a5311e868953df8e73ce76c9403bc7 | Python | 7,761 | 207 | """A-RAGGED-DOCS: pass-vs-step teaching honesty + the episode pass-axis disclosure.
Pins the foldB D11 docs-honesty fix (OPUS r3 R3-7): the shipped
``pass_variance`` example taught "variance explodes late in the sequence" as
``passes=[8, 9, 10]``, which is FALSE on any model whose layer is not called
at every step — p... |
e6a6b6dbd440677b204275473037fa448e090b9e5d0ac48e7696998d0820685e | Python | 7,762 | 224 | # Copyright (c) 2021 PaddlePaddle 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
162dc8936f900f1506292d83d54bfab58889a005f8bc7ba9f48a415eaa404952 | Python | 7,763 | 195 | '''
K-Folding script
author: obanmarcos
'''
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
from utilities.folders import *
... |
84fefaa9ab8ec4ca78846aadc74eaaef7737522915cb79d7ec03305be872474d | Python | 7,763 | 294 | from typing import List, Tuple, Dict, Union, Optional
import argparse
import logging
from pathlib import Path
from pprint import pprint
import numpy as np
import numpy.typing as npt
from ase import units as ase_units
import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import torch... |
534dc4a0a019bae47362a7c1a111ef3478269fdafc2ae499c1c394c746fdb542 | Python | 7,767 | 176 | import copy
import json
import os
from collections import OrderedDict
import PIL.Image
import numpy as np
import torch
import torchvision
from torch.utils.data import Dataset
from datasets.basic import MultiSiteDataset
from utils.project_utils import get_platform_specific_value
class MidlineDataset(MultiSiteDataset... |
d7be79a02ef105a7d8a008c50f078cd4239d2ed93f8ffcc14f8afb234146eb21 | Python | 7,768 | 265 | import locale
locale.setlocale( locale.LC_ALL, 'en_US.UTF-8' )
import re
import pdfplumber
import pandas as pd
import dateparser
try:
from local_extractor.utils import common_utils
from local_extractor.utils import custom_exceptions
from local_extractor.utils.table_concatenation import concatenate_tables... |
f7e6f60b6eeb3248a677352fffef93f1b562530d49bdd64bad03e32113c2bcae | Python | 7,768 | 155 | # -*- coding: utf-8 -*-
import os
import yaml
import argparse
import numpy as np
from utils import check_folder, read_yaml, save_yaml, write, get_subject_name, get_output_name, aggregate_cv, create_maps, fetch_masker, fetch_data, get_nscans
from utils import get_splitter_information, get_compression_information, get_d... |
b0e13c32719827f583fc0c240bc552c623b0bab70a740bfe9431880f8ec0a6cd | Python | 7,770 | 281 | """Utility functions for working with data arrays."""
from copy import deepcopy
import numpy as np
from scipy.ndimage import gaussian_filter
from spiketools.utils.extract import create_nan_mask
from spiketools.utils.checks import check_array_orientation, check_param_options, check_bin_range
#######################... |
ad920c19289a2adece3d1ac3ce1cd4bfa2f5dbf5b8fff16318badab4b36a093b | Python | 7,771 | 133 | # pylint: disable=line-too-long,too-many-lines,missing-docstring
"""UCF101 video action classification dataset.
Code adapted from https://github.com/open-mmlab/mmaction and
https://github.com/bryanyzhu/two-stream-pytorch"""
import os
from ..video_custom import VideoClsCustom
__all__ = ['UCF101']
class UCF101(VideoCls... |
2d2e8d13ddd5b3609e9209c3106bde13653995658d74c0c235b6da539d810b7e | Python | 7,773 | 260 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Lighting(_BaseTraceHierarchyType):
_parent_path_str = "streamtube"
_path_... |
46f207123dc4a23e9a6b533956dc078bbd6ae75ea81b0b94087cc9addce2aa68 | Python | 7,773 | 260 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Lighting(_BaseTraceHierarchyType):
_parent_path_str = "isosurface"
_path_... |
87c657640f756b947f7844177c076ede9e4f4e8a168373186a08b9a283572e10 | Python | 7,774 | 190 | """Quickstart real-model rows (F17 B17; memo section 6).
Real checkpoints, never toy stand-ins: resnet18 (IMAGENET1K_V1), gpt2 (real
tokenizer), CLIP (the multi-input boundary rider). Missing libraries skip;
missing checkpoints on a provisioned box are setup failures, never skips.
All cost assertions are counters, nev... |
a82499afaf8c848fe7d231d44b50fbdf201fa648143b999549a52f567a58af2e | Python | 7,774 | 200 | """F12 pins: the Stage-0 deterministic audit and the R0 baseline runner.
Stage-0 runs with no model in the loop; a failure is a build bug and never
reaches an evaluator. The R0 leg here baselines the geometry gate and the
shipped headlabel family on the toy corpus (the real-corpus R0 legs are
D03's, per the gallery sp... |
ed0d87d30259bdbad9ffcd0dff0b2aecf4e73077e85a2c9a873e74053332ed70 | Python | 7,775 | 157 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
1945ef18b5998f1fd7b037c0bbfd04792088c9ea9128342d0dea03b8091ee853 | Python | 7,777 | 180 | """
Centralized path configuration for the AD confirmatory tool testsuite.
Two filesystem roots are required to run this codebase:
AWARENESS_DATASETS — directory containing raw EEG cohort data
(ds004504/, ds006036/, Brain_Lat/, figshare_5450293/,
ds003775/, LEM... |
c6c6fe0bffba11d57e9dc7c8d3514c03266abbada7260fd9b9c627e2c5d6b8eb | Python | 7,777 | 214 | #!/usr/bin/env python3
import csv
import os
import re
import subprocess
import zipfile
from multiprocessing import Pool
import progressbar
import sox
import unidecode
from deepspeech_training.util.downloader import SIMPLE_BAR, maybe_download
from deepspeech_training.util.importers import (
get_counter,
get_im... |
c0b7c64bdd393be9a4dd49c558b0b54fd678ce90a33cff8ddf25e0bdf1aff49e | Python | 7,779 | 210 | """Tests for the Analysis portal app -- real (non-mocked) end-to-end
coverage against the package's bundled DATA_DIR reference dataset, since
`_AnalysisController` relies on `GraphRegistry`/`analysis_helpers`
functions whose failures (registry construction, plot availability,
figure saving/rendering) are all silently s... |
c8c707d68e20788753e6ed815cf2e23fdc5a2694de42724a1dcf97a06528cdca | Python | 7,779 | 183 | from __future__ import annotations
import logging
import threading
import time
from collections import OrderedDict, defaultdict
from collections.abc import Generator
from typing import Callable, Optional
import grpc
from grpc import RpcError
from minknow_api import protocol_service
from bream4.device_interfaces.devi... |
103c12049853f5cb3ea29401a55410910ac4ea61314fc125a7be338576ee7218 | Python | 7,780 | 195 | '''
K-Folding script
author: obanmarcos
'''
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 dlutils
from utilities.folders i... |
6d7df8d7727044c323e385fef8ac1a714e0de18f28f1e89a193912ad83a30806 | Python | 7,780 | 194 | import logging
import os
from datetime import datetime
from autouri import GCSURI, S3URI, AbsPath, AutoURI
from .cromwell_backend import BACKEND_AWS, BACKEND_GCP
logger = logging.getLogger(__name__)
class CaperBase:
ENV_GOOGLE_APPLICATION_CREDENTIALS = 'GOOGLE_APPLICATION_CREDENTIALS'
DEFAULT_LOC_DIR_NAME ... |
a91e0745c4405fe00c1755d48effdf7d41e9c8dd665892b7d64bffd1a2a8e8d7 | Python | 7,780 | 269 | """Shard codecs: safetensors default behind the manifest field (item 11).
The shard format is a MANIFEST FIELD (extract D1), so a format change is a
value change, never a layout break: ``safetensors`` is the v2 default
(keyed row slicing, third-party readable, bf16/fp8 byte-exact), ``pt``
stays readable forever and wr... |
ea822cbac8769d19d46ca562cc9e6a4d54013eab46e023be3f902330692e4689 | Python | 7,780 | 245 | import socket
from types import SimpleNamespace
from unittest.mock import patch
import pytest
from celery.utils.threads import (Local, LocalManager, _FastLocalStack, _LocalStack, bgThread,
bound_open_broker_sockets, default_socket_timeout)
from t.unit import conftest
class test_def... |
f2ca835b393b6727b35a62a46725025dc285b135e5eda4d4d59cd42e012525d3 | Python | 7,780 | 240 | """System information utilities."""
from __future__ import annotations
import os
import posixpath
from math import ceil
from typing import NamedTuple
from kombu.utils.objects import cached_property
__all__ = (
'load_average', 'df',
'AUTO_CONCURRENCY', 'is_auto_concurrency', 'available_cpu_count',
'cgroup... |
f52a195109b4314e5d50328e04fd89738728c0d7e3a21105eebff811c047f043 | Python | 7,780 | 202 | import numpy as np
from functools import partial
from .constants import *
from mne.io import Raw
from os import path
import pickle as pkl
class FrequencyBands(object):
def __init__(self, signal, bands):
self.data = {}
self.names = list(bands.keys())
for band_name, filter_pars in bands.items... |
5a0ac9e39bb866049742e61865cff759e9d3248675c071ec99507d0dfa8ac68e | Python | 7,782 | 209 | import os.path
import tempfile
import pytest
import tensorflow as tf
from tensorflow.python.eager import context
from keras.src import backend
from keras.src import callbacks
from keras.src import layers
from keras.src import losses
from keras.src import metrics
from keras.src import optimizers
from keras.src import ... |
751b3ff1c1b2a177cd2f55eb36d2d025bf92a2e4a09d13c78c71f0a554564be7 | Python | 7,782 | 143 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
1addcdba0821dc31c1513e17b62da0b35c184744e4591a71e6338389cdb19bf3 | Python | 7,783 | 214 | """
This code creates simulated data for fig in Methods.
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import butter, filtfilt, hilbert
from scipy.stats import vonmises
def create_signal_nzm(n_samples, fs, nzm_coeff):
"""
Generates alpha signals with non-zero mean profile
:... |
eddd3f39a13073b2d4cf810b5d5aae1181bce77a2d725af2519d8ee93d0d2ac7 | Python | 7,783 | 265 | from typing import ClassVar
import equinox as eqx
import jax.numpy as jnp
from cvsx.unit_conversions import convert
class PressureVolume(eqx.Module):
_e: float
v_d: float
v_0: float
_lam: float
p_0: float
_e_scale: float = 100.0
_lam_scale: float = 10.0
def __init__(self, e, v_d, v... |
f1e86f8675ef7750901278753613de8b7e930a60b911f214d397151253516c73 | Python | 7,783 | 220 | import warnings
from collections import OrderedDict
import copy
import pathlib
import errno
import numpy as np
from .flblend import FlBlend
from .formats import load
from .util import equal_states, dict_update_nested
class DataSourceSignatureMismatchWarning(UserWarning):
pass
class DataChannel(dict):
"""O... |
2a1dd927027d24061d51bc29bb9960950d14eb6b761f34540b668e10575d9b27 | Python | 7,785 | 198 | from __future__ import annotations
import pytest
from pytest_celery import RESULT_TIMEOUT, CeleryTestSetup, CeleryTestWorker, CeleryWorkerCluster
from tenacity import retry, stop_after_attempt, wait_fixed
from celery import Celery, signature
from celery.exceptions import SoftTimeLimitExceeded, TimeLimitExceeded, Work... |
dab80dc8e01de73a251676abd6675ba40e96d84c64160a2710755691bc417648 | Python | 7,786 | 206 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
10_coverage_gate.py — 蛋白质组衰老时钟的「覆盖率闸门」
------------------------------------------------------------------
这是整个路线 A 里最重要的一个前置检查，必须在跑任何模型之前执行。
原因：
各时钟权重是在 UK Biobank Olink Explore 3072（约 2900 蛋白）上训练的。
一旦你手上的数据集是 Explore 1536 / Target 96 / 或其他平台，
权重所要求的蛋白会大量缺失，而 pro... |
09c4523fc1bdff2100d130e35311227bacf7ca8e0a3fa6ea80191751a75f3899 | Python | 7,787 | 217 | from types import SimpleNamespace
from more_itertools import chunked
import numpy as np
from permacache import permacache, stable_hash
import torch
from modular_splicing.data_for_experiments.standardized_sample import (
standardized_sample,
)
@permacache(
"modular_splicing/motif_perturbations/motif_statisti... |
4987cf977f2f737e3faf87733a0fb5516a263a47898294a7612274d9a5cd84eb | Python | 7,788 | 208 | #!/usr/bin/env python
# coding: utf-8
import numpy as np
import pycuda.gpuarray as gpuarray
from pycuda.compiler import SourceModule
import pycuda.driver as cuda
def _build_kernel():
code = """
__global__ void Funktion(short *verts1, char *arr1, char *arr2, char *mask2, char *lock1, char *lock2, int xsh1, int... |
8ae5385dea6310bb3cb8f689ce1331c6b920c74f762adef8168d37eeefba1faa | Python | 7,789 | 206 | import tensorflow as tf
import tensorflow_datasets as tfds
from cvnn import layers
import numpy as np
import timeit
import datetime
from pdb import set_trace
try:
import plotly.graph_objects as go
import plotly
PLOTLY = True
except ModuleNotFoundError:
PLOTLY = False
# tf.enable_v2_behavior()
# tfds.di... |
fda57cf0cb4746ffb43a1e8004ac2ba746f8880576877ca5bd7e5344d7276090 | Python | 7,789 | 230 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import copy
from functools im... |
bb5b4b1b7c1d1c122c22fb435146820125589e9a4bc3190577b5cf80cecea024 | Python | 7,790 | 157 | #!/usr/bin/env python3
import os,sys,matplotlib,zipfile,argparse,string
matplotlib.use('Agg')
from pylab import *
from lefse.lefse import *
import random as rand
colors = ['r','g','b','m','c']
def read_params(args):
parser = argparse.ArgumentParser(description='Cladoplot')
parser.add_argument('input_file_1', metav... |
22973e8a061a4a64e3fb8a923d0ea9bd2d5d6e11c5886692b911424b6114c07a | Python | 7,791 | 264 | # --- 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 Lataxis(_BaseLayoutHierarchyType):
_parent_path_str = "layout.geo"
_pat... |
28d8616ef040b4bc2e342f59b63d6b8e65bc147b694bfd673f70aeaebd521c31 | Python | 7,791 | 187 | """Writer-contract lockstep: the committed contract of record vs the live tree.
Three guarantees (ecosystem MEMO 3.1/3.3/3.4, megaplan P05):
1. LOCKSTEP -- regenerating the writer contract from the live tree reproduces
``torchlens/schemas/writer_contract_v<TLSPEC_VERSION>.json`` exactly. Any persistence
contrac... |
629796c37ce3ce1764d788bbcca137f8a3b51128e5b8f94ec3cfc6739aadb0cf | Python | 7,791 | 264 | # --- 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 Lonaxis(_BaseLayoutHierarchyType):
_parent_path_str = "layout.geo"
_pat... |
c045a2c0b468f6cb88d3bceebf671c30b069bb05df0cf99cc870f11cb0c50ed5 | Python | 7,792 | 237 | """Comprehensive storage-mode behavior tests for fastlog."""
from __future__ import annotations
import ast
from pathlib import Path
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens._io.streaming import PARTIAL_SENTINEL
from torchlens.fastlog import CaptureSpec, PredicateError, R... |
09ff0070ea9704fa2578e84b23c79993fa649d5489043b0add8b816af1ce497c | Python | 7,794 | 204 | """B3 + B8 + B9: honesty batch, overlay repair, escrow bound + address preflight.
Every raise site added by lane F34 gets its provoking test here (census law):
``node_overlay_zero_match``, ``node_overlay_partial_match`` (warning),
``cone_origin_invalid``, ``site_table_empty``, ``escrow_budget_exceeded``.
"""
from __f... |
642e17bb36c132f1b27e3044aecde77ad85f5310bc692b356a5ccc5c42f7e38c | Python | 7,795 | 212 | # coding=utf-8
# Copyright 2023 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... |
e95bd11af6049d2cd00d8a8218e4dc4ca29fde0741506423be38c03590e7346b | Python | 7,795 | 222 | from typing import Any, Union, Optional
import numpy as np
import torch
import torch.nn
from torch.nn import Sequential, ReLU, Linear, LayerNorm
try:
from torch.nn import LazyLinear
except ImportError:
print("torch version is %s. Lazy modules are turned off." % torch.__version__)
#from torch_scatter import sca... |
562dd1093b3a371819227db97548f1b57450d196229f1656b347d329d191c6fa | Python | 7,796 | 213 | """T7 (grind-p3): getitem mixed-key variants stay oracle-exact, and check()
probes exact claims on non-windowed axes.
HIGH variant battery: the rank-changing getitem fix (slice affines plus
recorded selection indices composed through both engines and both query
walks) is pinned against an independent autograd oracle f... |
27b3fa1507f6a55420f2ed6f57e9ea716189d18d7f715f21c5f14f7053c1f5cd | Python | 7,798 | 197 | """Regression tests for the cert10 (round-10-prep) intervention hardening fixes.
BLOCKER -- ``_record_predicate_intervention_spec``
(``torchlens/backends/torch/ops.py``) built its dedup cache key from
``repr(decision.hook)``. When the fired helper is a ``HelperSpec`` carrying a live
``torch.Tensor`` argument -- i.e. T... |
da47f990357818787095922642fb7e2b97f79f8a6a9ed99567dfdb76c48160a2 | Python | 7,800 | 220 | import numpy as np
import torch
import torch.nn as nn
###########################################
# THE HIGH-TO-LOW-DIMENSIONAL TRANSFORMER #
###########################################
class A(nn.Module):
def __init__(
self,
network_dim,
data_dim,
hidden_features=256,
hid... |
7fb0b75fe448b07a1c909d3ab77bc81fd2cf016fc43bf1b590b50dd1c26dd247 | Python | 7,804 | 242 | import gzip
import numpy as np
from Bio.PDB import *
try:
from Bio.PDB.Polypeptide import protein_letters_3to1
def three_to_one(s):
return protein_letters_3to1[s]
except ImportError:
from Bio.PDB.Polypeptide import three_to_one
from Bio.PDB.Polypeptide import is_aa
aa_modif={"TRN":"TRP", "CSO":"CYS... |
530320c3b6f5d35926c00ccf97ff525a8ff4dc8ddc01aa44b03b6546f14256ff | Python | 7,805 | 167 | from torchvision.transforms import transforms
from data_aug.gaussian_blur import GaussianBlur
from torchvision import transforms, datasets
from data_aug.view_generator import ContrastiveLearningViewGenerator
from exceptions.exceptions import InvalidDatasetSelection
from PIL import Image
import pandas as pd
from sklearn... |
79286aa73ec2e6c39afd68aeaf6b7f39b6c16c07fd1a62c0597d8dd14b514863 | Python | 7,806 | 170 | import logging
from typing import TYPE_CHECKING
from galaxy import model
from galaxy.jobs.runners import JobState
from galaxy.util import now
from ._safe_eval import safe_eval
if TYPE_CHECKING:
from galaxy.app import GalaxyManagerApplication
from galaxy.jobs import ResubmitConfigDict
from galaxy.jobs.runn... |
3e77848310d257f5be73c150877103c1a0e970ec81183dbc297a933253720553 | Python | 7,809 | 215 | '''
Keras implementation of B networks
'''
import tensorflow as tf
def b_layer(x, filters, kernel, layer_num, pooling=True):
'''Base layer for B models
'''
if pooling:
x = tf.keras.layers.MaxPool2D(
pool_size=(2, 2),
name='MaxPool_Layer_{}'.format(layer_num))(x)
x = t... |
9339a72e8b2557fd5cf78041480eb8574ccdc70bf891410d6c33c72270ee9803 | Python | 7,810 | 213 | """
Base UI for data tables.
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Sof... |
adb0d2f099ec931755deaf98e2047a38faa52584f177c29357e45cf329e1162e | Python | 7,810 | 273 | import random
import time
import sys
import itertools
import multiprocessing
import array, numpy, rpy2.robjects as ro
import rpy2.robjects.packages
from rpy2.robjects import Formula
from functools import reduce
n_loops = (1, 10, 20, 30, 40)
def setup_func(kind):
#-- setup_sum-begin
n = 20000
x_list = [random.... |
2aab80bf27c96aa3c8f181251dc79ed8c45b1bf91fdd073bcd1bddccfd6c6d07 | Python | 7,811 | 189 | from typing import List, Optional, Tuple, Union
import numpy as np
from anndata import AnnData
from spateo.configuration import SKM
from .methods import generalized_procrustes_analysis, paste_pairwise_align
from .transform import paste_transform
from .utils import _iteration, downsampling
@SKM.check_adata_is_type(... |
531220c210634c33f7ee61c553c204dce02f99d170296a8f4d709dc3d932caf8 | Python | 7,811 | 210 | import datetime
from flask_restplus import Namespace, Resource
from flask_login import login_required, current_user
from flask import request
from ..util import query_util, coco_util, profile, thumbnails
from config import Config
from database import (
ImageModel,
CategoryModel,
AnnotationModel,
Sess... |
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