sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c641be1bec61985e880f542684c323850000eb4ba0c772b19cf735f2301ed4a6 | Python | 7,386 | 243 | ##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
## This file is par... |
d17f917468f88e69d43acac54881da1d4785173e88d0e31d5453fb768fe195d5 | Python | 7,386 | 199 | from __future__ import annotations
import warnings
from functools import partial
from typing import Any, Callable
import torch
import torch.nn as nn
from torch import Tensor
from lightly.models import utils
from lightly.models.modules.masked_vision_transformer_decoder_timm import (
MaskedVisionTransformerDecoder... |
f4d5af5cfd64b58775d2cea6132cd1fa29f1c23b8d02712fad45e068300cb96d | Python | 7,386 | 184 | #
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.parameter import Parameter
from torch.nn.modules.module import Module
from .layers import AvgReadout, Discriminator, Clusterator, Discriminator_cluster, full_block, GraphConvolution, \
InnerProductDecoder
class conST(nn.Module):
... |
82be6116b0f352d19fa7fd2dbb4b25973232af78cc41e8089059a50dab90271c | Python | 7,388 | 221 | from distutils import log
import distutils.command.sdist as orig
import os
import sys
import io
import contextlib
from setuptools.extern import six
from .py36compat import sdist_add_defaults
import pkg_resources
_default_revctrl = list
def walk_revctrl(dirname=''):
"""Find all files under revision control"""
... |
14ca336ab025a91153ca3302246d66e1f4b3b04485d5e96c20335c7a0088d8e1 | Python | 7,390 | 204 | """Tests for the Trace summary feature."""
from __future__ import annotations
from collections.abc import Generator
import pytest
import torch
from torch import nn
import torchlens as tl
class TinySummaryModel(nn.Module):
"""Small model with stable top-level module names for summary tests."""
def __init_... |
01cde58342c50ebadfc081288854325d02b40af3ed2b9343e72f38bd0e8d0977 | Python | 7,391 | 181 | """02. Train SiamRPN on COCO、VID、DET、Youtube_bb
==================================================
This is a Single Obejct Tracking tutorial using Gluon CV toolkit, a step-by-step example.
The readers should have basic knowledge of deep learning and should be familiar with Gluon API.
New users may first go through `A ... |
722ccb208b460c9ad8c06e6fcc5fa208fba4065fe971bf6d475885f24c61f6e3 | Python | 7,392 | 212 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from tgcn import ConvTemporalGraphical
from graph_part_remove_joint_upper_limb import Graph
class Model(nn.Module):
r"""Spatial temporal graph convolutional networks.
Args:
in_channels (int): Number... |
f7a34713cbaac7d7412f0ea4d01c9ab1b3d2287f1e8dd99c4f38ff92a978628e | Python | 7,393 | 238 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft
# Licensed under the MIT License.
# Written by Bin Xiao (leoxiaobin@gmail.com)
# Modified by Bowen Cheng (bcheng9@illinois.edu)
# ------------------------------------------------------------------------------
fro... |
6dd840d98abbc47887980c6d16474fca3ef453daf3d7fcfbba96bd1d00043b38 | Python | 7,394 | 188 | import yaml
import configargparse
import os,re
import pandas as pd
from pathlib import Path
import matplotlib as mpl
from matplotlib import font_manager
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib.ticker import ScalarFormatter
class ScalarFormatterClass(ScalarFormatter):
def _set_for... |
a0817ea24c95744fea96743176529768e9c1d26e9c4af9a0173b372abba0925c | Python | 7,394 | 177 | #!/usr/bin/env python3
"""
Dx BK — Single-channel + random-K-channel sweep redo (proper per-fold)
=======================================================================
Two analyses re-run under the proper per-fold deployment-mode
pipeline using cached figshare per-channel ablation extractions:
A) Single-channel a... |
382600199bbd91202fb294930a2e27105099703a9f8277d30e857c219639c7af | Python | 7,395 | 181 | import pylustrator
pylustrator.start()
import os
import tensorflow.keras as keras
from tf_spiking import DenseLIF, DenseLIFNoSpike, IntensityToPoissonSpiking
from tf_spiking.helper import TrainingHistory
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from copy import deepcopy
... |
4971fa7dae548e1b13c51f34d3f81e5f1f8a28225500150d5df6e686585649df | Python | 7,395 | 191 | """
'Oscillations' as Peaks
=======================
Exploring the idea of oscillations as peaks of power.
This example uses the
`neurodsp <https://neurodsp-tools.github.io/>`_
module for time series simulations & analyses.
"""
##########################################################################################... |
9b8f5d75f1715df3b1aa076de165345d30ec036428a655a368d93f7b0b528964 | Python | 7,396 | 149 | # coding: utf-8
# 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... |
a09eac518472bf6082ac0525684ff54bd409adadc3332cb3c3d86cd4ed9560bb | Python | 7,397 | 204 | """
Execution of simulation runs in a separate process.
Launches a run as a subprocess so that long simulations do not block the
caller, and reports back when the run completes.
"""
from __future__ import annotations
from typing import Any
import argparse
import subprocess
import pandas as pd
from .. import util
fr... |
dfcb5578cff354adf7c1b210261b5ecba39ff944cb1eb57f866f6e9c67932170 | Python | 7,397 | 190 | #!/usr/bin/env python3
"""
Script to detect the network IP range/subnet for ethoscope devices.
This script analyzes the network interfaces and determines what IP range
the ethoscopes are likely to be on, which can be used for SSH configuration.
"""
import netifaces
import ipaddress
import socket
import sys
from typin... |
118c321db63c4d7936f6d3a997f1503b0e41041925f35ff7c90ee1cf45fdea0b | Python | 7,398 | 259 | # BASE
URL = "https://download.bbbike.org/osm/bbbike"
suffix = ".osm.pbf"
class Cities:
available = ['Aachen',
'Aarhus',
'Adelaide',
'Albuquerque',
'Alexandria',
'Amsterdam',
'Antwerpen',
'Arnhem... |
76a6ca9d791af4eda28b7b1761c638a37c6dd2bb18568c15b6a8ce4e973dc593 | Python | 7,398 | 188 | import unittest
from numpy import max, abs, ones, zeros, hstack, sqrt, finfo
from cantera import gas_constant
from spitfire import ChemicalMechanismSpec as Mechanism
import pickle
import cantera as ct
ct.suppress_thermo_warnings() # because we are faking heat capacity polynomials
species_decl = list([ct.Species('A',... |
51c8ffd29d2925df72de33a51859c6024ab4453677053362cdfdcbe8b7a3a1cc | Python | 7,399 | 122 | """This script estimates TRFs for several models and saves them"""
from pathlib import Path
import re
import eelbrain
import mne
STIMULI = [str(i) for i in range(1, 13)]
DATA_ROOT = Path("~").expanduser() / 'Data' / 'Alice'
PREDICTOR_DIR = DATA_ROOT / 'predictors'
EEG_DIR = DATA_ROOT / 'eeg'
SUBJECTS = [path.name fo... |
b937568ed055bf4cc0c90a9f07dbb8b58d4f3693c9bc1940137a0b4b9b0a0b23 | Python | 7,401 | 190 | """
Unit tests for ImgMaskROIBuilder.
Tests ROI generation from grayscale image masks where each contour becomes an ROI.
"""
import os
import pathlib
import unittest
from unittest.mock import patch
import cv2
import numpy as np
from ethoscope.roi_builders.img_roi_builder import ImgMaskROIBuilder
# Get the absolute... |
2cca8d7699a6ed84fd1f2d0d88c5ebb024af38ae47f3414cd9d94a815542ecac | Python | 7,402 | 198 | """History schema tests: vocabularies, payload coherence, merges (D4-D8)."""
from __future__ import annotations
import pytest
import torch
from torchlens.observability import (
PHASES,
PRESENCE,
STREAMS,
HistorySchemaError,
ObservationRecord,
RunRecord,
SiteRecord,
Spine,
StepBloc... |
f851a0b54704e9dfdcbe7124e5a962a6f9d34a379552d14a238f30a208ab8c26 | Python | 7,402 | 200 | # -*- coding: utf-8 -*-
# @Author: gviejo
# @Date: 2022-01-17 14:10:40
# @Last Modified by: gviejo
# @Last Modified time: 2023-10-27 16:23:54
import numpy as np
import pynapple as nap
from scipy.signal import butter, lfilter, filtfilt
def _butter_bandpass(lowcut, highcut, fs, order=5):
nyq = 0.5 * fs
low =... |
cfc7d9497c1e0fd6a8bd450acb3b038f7ce0f6aaebc788bea15aad835b579e5d | Python | 7,403 | 188 | import torch
import os
import random
import pandas as pd
from torch_geometric.data import InMemoryDataset
from rdkit import Chem
from tqdm import tqdm
from typing import List
from .conf_ensemble_dataset import ConfEnsembleDataset
from bioconfpred.conf_ensemble import ConfEnsembleLibrary
from bioconfpred.data.sources i... |
199fd060ad39899ff42ab3dcf49d105e525ca0e598ab453b423060df202d60e1 | Python | 7,407 | 205 | """Output Biopython SeqRecords and SeqFeatures to GFF3 format.
The target format is GFF3, the current GFF standard:
http://www.sequenceontology.org/gff3.shtml
"""
import urllib
from Bio import SeqIO
class _IdHandler:
"""Generate IDs for GFF3 Parent/Child relationships where they don't exist."""
def __i... |
95b5bd55ba5c0e299495dc4a222364d803d5361f59b988386e3c945baa4c812f | Python | 7,407 | 192 | import os
import numpy as np
import copy
import torch
from openbabel import openbabel, pybel
from rdkit import Chem
from rdkit.Chem import rdMolTransforms
from rdkit.Chem import AllChem
from scipy.spatial.transform import Rotation
from sklearn.cluster import KMeans
from src.utils.dist_to_coords_utils import get_mask_r... |
a4687bc3f30717e51b64e079804c47112cc258e51755808b56b6e2d1ca6a0fe6 | Python | 7,407 | 211 | # 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... |
f9b4f12eeed88417ac8a212b1ca5bf6f60d6096bb9865c62bfd19fe0d0cd52ec | Python | 7,409 | 176 | import numpy as np
class Graph():
""" The Graph to model the skeletons extracted by the openpose
Args:
strategy (string): must be one of the follow candidates
- uniform: Uniform Labeling
- distance: Distance Partitioning
- spatial: Spatial Configuration
For more informa... |
c151d1ab2ed347cc0a8a92b6c828a1ff08068c91a35bb11d4e782d10f6cc5f29 | Python | 7,410 | 252 | import seaborn as sns
from .. import settings
import matplotlib.pyplot as plt
from typing import Union, Mapping, Sequence, Iterable, Optional
from ._utils import _plot_seaborn, _violin_long
import xarray as xr
def countplot(
sdata: xr.Dataset,
vars: Union[str, Sequence[str]],
groupby: Optional[str] = None... |
b50d57fccb9be3bb7ddbe3cc46172fa80196feccf2c8f548f2a8e1e48822af4c | Python | 7,411 | 214 | """
X-ray Photoelectron Spectroscopy (XPS) Datatypes
Datatypes for surface analysis data produced by X-ray photoelectron
spectroscopy (XPS, also known as ESCA). Two related formats are provided:
* :class:`Vamas` - the ISO 14976 VAMAS standard plain-text format, the
open interchange format for surface analysis data ... |
e65448a90333d590deed9c23df2843d8437c7e9200e5bb5274464d5f66fde77a | Python | 7,411 | 182 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
327f1ef6d9ac1ca6846b23f6e71cffec705fb763ab5aa8453bf76d64c4ed517c | Python | 7,412 | 220 | import os
os.environ['DTORROOT'] = '/DATA/forLishan/randomddd'
#os.environ["CUDA_VISIBLE_DEVICES"] = "0"
from dtor.utilities.utils_stats import stats_from_results,roc_and_auc
from sklearn.metrics import roc_curve, auc
import numpy as np
import argparse
import torch
from dtor.utilities.utils import set_plt_config
from d... |
fc70ba48e0d952331e20d4cc7ce7904f18cf2550a196908397bd90f32046bf9d | Python | 7,414 | 199 | import numpy as np
import scipy
import brian2.only as br
import analysis
import os
IPSC_timestep = 20 * br.us
IPSC = np.genfromtxt("data/PC_IPSC_20ms.csv")[1:] # 20 us timestep
IPSC = IPSC / max(IPSC)
EPSC = np.genfromtxt("data/MF_EPSC_20ms.csv")[1:]
EPSC = EPSC / max(EPSC)
def run_DCN_wave(**k... |
1c7461be48e6e8ada709cccd00e8a6097f12a6b4a3d2b8a52d4b68bc94c3c034 | Python | 7,415 | 234 | import os
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
import argparse
import numpy as np
from pyteomics import mgf, mass
from dataclasses import dataclass, asdict
import tensorflow as tf
import tensorflow.keras as k
from tensorflow_addons.layers import InstanceNormalization
from utils import *
print(tf... |
c89b1e55f1b49f5105b6ab13e9afd28b55d64fbf3d2409c1f5557fbe505c057f | Python | 7,416 | 189 | from __future__ import annotations
import warnings
import torch
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Module, Parameter
from lightly.models.modules import center
from lightly.models.modules.center import CENTER_MODE_TO_FUNCTION
class DINOLoss(Module):
"""Implementation o... |
9f7490d815e586a685122290aff9ea61a6d10514d5996d96ff911db7d62c6602 | Python | 7,417 | 187 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 1 11:37:26 2021
@author: Audrey Mazancieux
This script estimates a general linear model (GLM) at the subject level for
all stimuli in the local-global task. Other regressors include V4 time serie,
movement parameters, and physiological regresso... |
6195ac80339e1c6c1c83a3b523ef0182cb297eb47adb13f07a1dcdb6d107547c | Python | 7,419 | 248 | # coding=utf-8
# Copyright 2025 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... |
a973ccb7e752a5705d9af01f16954fa044807c867ed6cd0a0d8693fe42870446 | Python | 7,420 | 235 | """
This module includes a dual classification method. Not used in the current
implementation of the MetalHawk, but will be included in a future version.
"""
from copy import deepcopy
import numpy as np
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import RobustScaler
class DualOutputClassifier(o... |
99abc9377e6e76c2464595583dbc56ceccfa26895f70cce105a91bd251d78244 | Python | 7,423 | 184 | from __future__ import print_function, unicode_literals, absolute_import, division
from six.moves import range, zip, map, reduce, filter
from ..utils import _raise, backend_channels_last
from ..utils.tf import keras_import, BACKEND as K
Conv2D, MaxPooling2D, UpSampling2D, Conv3D, MaxPooling3D, UpSampling3D, Cropping2... |
a38a271d6280e1e72c275ae138c91dfe9dacaa4790e80f3188571e2a877a1d9b | Python | 7,423 | 200 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 21 15:09:10 2022
@author: fcheng
"""
#coding:utf-8
import os
import numpy as np
import PIL
from PIL import ImageFont
import cv2
from plot.image_process import img_process, gammaCorrection
# save dirs
save_dir = "./results/plots/quick_test"
i... |
47a69a3f1ffe9674cfa4d4b1f26a68d454f4af7bc2d4a96ebb7642b886bae416 | Python | 7,425 | 223 | from typing import Any, Callable, Optional, Union
from pl_bolts.datamodules.vision_datamodule import VisionDataModule
from pl_bolts.transforms.dataset_normalizations import emnist_normalization
from pl_bolts.utils import _TORCHVISION_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _TORCHVISION_AVAIL... |
600fe763e700c77569beb37a0c28dea64d087450a12ca7c6c2f3c2067b32fd0d | Python | 7,425 | 206 | """Ledger contract lockstep (row 0.8): validation, red-capability, projection diff.
The ledger's closed vocabularies and per-state teeth are enforced here, every
rule is red-capability-proved with planted rows (a gate nobody has proved can
fail is not a gate -- memo section 9), production capability ids are
REFERENCED... |
60f8d83b935a585076e0fa037abbb5fc53e38eff2449745bea40b7eb42c7cba9 | Python | 7,426 | 249 | import numpy as np
import dateparser
import camelot
import tabula
import pdfplumber
import pandas as pd
import math
import gc
from pdfminer.high_level import extract_pages
from camelot.core import TableList
from utils.tabledetection.tabnet import ExtractTable
def clean_numbers_str(text):
chars = ['%', '*']
... |
a1730e0b612aa5994c94fa9aa710a0f97043aaae326f2f8beccc7cae9c2b5329 | Python | 7,426 | 193 | from pathlib import Path
from typing import Literal
import h5py
import numpy as np
import pytest
from anndata import AnnData
from mudata import MuData
from scipy import sparse
import muon as mu
@pytest.fixture
def filepath_hdf5(tmp_path: Path) -> str:
return str(tmp_path / "mofa.hdf5")
@pytest.fixture
def mda... |
a3f7fb091e99ca5d0dd7ce7d7ce0cd09325dac8e095cfc23537131a3e292468f | Python | 7,426 | 209 | import pickle
import os
import numpy as np
import sys
import torch
import torch.nn.functional as F
from torchvision import transforms, utils
from src.utils import save_gif, save_png, save_video, convert, convert_image,\
save_apng
from src.html import make_simple_index, make_list_index
def single(stylegan_weights... |
5928337a2049fbbb6ca615e21ac8a080df015257f476955f648ddc6ba450d593 | Python | 7,427 | 266 | from __future__ import annotations
from collections.abc import Sequence
from typing import Optional, Union
import numpy as np
import pandas as pd
from bream4.device_interfaces.devices.base_device import BaseDeviceInterface
from bream4.toolkit.analysis.metrics.waveform_utilities import waveform_triangle
from bream4.t... |
208dc91e9d535e00b49769a17491027cb5a6322945cb0c27d35ad6101b944c53 | Python | 7,428 | 219 | import itertools
import re
import attr
import h5py
import numpy as np
class MultiH5File:
"""
Concatenate the files in the list, using higher indices for each
type as the list progresses.
E.g., if file one has keys X0, Y0, X1, Y1 and file two has keys X0, Y0, X1, Y1,
then the resulting fi... |
080fa9cc6af157d466c1716da7fde4d9e9c2aba9c29d892bd40ffab2a4f3ede8 | Python | 7,429 | 178 | # -*- coding: utf-8 -*-
from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
from collections import namedtuple
from ..utils.tf import keras_import, BACKEND as K
Model = keras_import('models', 'Model')
Input, Conv3D, MaxPooling3D, UpSampling3D, Lambda, Multiply = keras... |
ebfc6d868b6809be5bc31d130822bc0454804bb2452dca0d61a966cf80e3cde2 | Python | 7,430 | 165 | from __future__ import division
from __future__ import print_function
import os
# disable autotune
os.environ['MXNET_CUDNN_AUTOTUNE_DEFAULT'] = '0'
import argparse
import glob
import logging
logging.basicConfig(level=logging.INFO)
import time
import numpy as np
import mxnet as mx
from tqdm import tqdm
from mxnet impor... |
1a885f12956e7c2d8c77d9b2c9ccc094a4f385fed7b4c56c491818d744f67040 | Python | 7,431 | 195 | import pandas as pd
import numpy as np
import random
import os
from torch.utils.data import Dataset
import numpy as np
from dtor.utilities.utils import expand_image
from dtor.utilities.utils import bbox3d, crop3d,pad_nd_image
from tqdm import tqdm
import pandas as pd
import torch
from sklearn.model_selection import KFo... |
3971481190b7cc34c84c3408b683e6cc3509dc9e544e02b6eabf4e100abd3716 | Python | 7,431 | 215 | # 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... |
7f18ad6a8e14616e07abb076e7c4ff700ab61f747614dd7e9b0772d77f30f1f1 | Python | 7,432 | 225 | #!/usr/bin/env python3
# coding: utf-8
"""
Created in April 2020
@author: Thomas Bonald <bonald@enst.fr>
@author: Nathan de Lara <nathan.delara@polytechnique.org>
"""
from typing import Union
import numpy as np
from scipy import sparse
from scipy.sparse.linalg import LinearOperator
from sknetwork.linalg import diagon... |
ed5c280750658d0ebe18935fa63f5710a1e1cf962ce8c1c248ef36cb05388b34 | Python | 7,432 | 194 | """
This script shows the training pipeline for k-fold training, without logging it via wandb.
"""
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
from keras import backend as K
from sklearn.model_selection import StratifiedKFold
from tf_spiking.helper import TrainingHistory
fr... |
df3a2c6c8eb1823c4961e46f4718e7643fe678b7a342d8e2aab209f26efac051 | Python | 7,433 | 231 | """Strict typed accessor behavior tests."""
from __future__ import annotations
import pytest
import torch
import torchlens as tl
from torchlens._errors import AmbiguousOpLookupError
from torchlens.data_classes.buffer import Buffer
from torchlens.data_classes.grad_fn import GradFn
from torchlens.data_classes.layer im... |
1259cc7e4a1db056b65ed36ae366cfa39967d9dce0e66d8abe683d6f125f2940 | Python | 7,436 | 220 | """Contains the core functionality of the lightly Python package."""
# Copyright (c) 2020. Lightly AG and its affiliates.
# All Rights Reserved
import os
from typing import List, Tuple
import numpy as np
import yaml
import lightly.cli as cli
from lightly.cli.embed_cli import _embed_cli
from lightly.cli.lightly_cli i... |
8dc5a9e2511904c43b3679d70ad6eb10e5fb1acd4e1aac7f448d3c669ea0bea3 | Python | 7,437 | 224 | """Focused tests for the non-blocking Explore preview worker."""
from __future__ import annotations
from dataclasses import replace
from pathlib import Path
from types import SimpleNamespace
import pytest
from larvaworld.portal.canvas_widgets.environment_models import LarvaPreviewFrame
from larvaworld.portal.explor... |
ee0e8507b052b60b03b9ec00c234aca6aae79816021405cb43339f79ffbc6182 | Python | 7,437 | 193 | #!/usr/bin/env python3
"""
File: export_masked_matrices.py
Created: 2022/07/11
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 tree.... |
90f649af873478467fb2772828ceb5492cd9fbbe8146dff7c1606fa03a1fc62c | Python | 7,438 | 192 | """Lazy-module entry tolerance and residual refusals (quickstart B13/B14).
The wave-1a all-verbs entry refusal flipped off on the memo's own signal
(4.4) when the numbers-truth lane landed the parameter completion unit, and
the BUFFER-side refusal flipped off with the F20 lazy-buffer completion
(A10-fix2 remainder): t... |
2cabae31b12b6dfa4b4fc30c8e03a5cb537a0dd69fc0552271c9e20ef0c4d737 | Python | 7,439 | 203 | """Mask RCNN default config"""
# pylint: disable=unused-variable,missing-function-docstring,bad-whitespace,missing-class-docstring
# from typing import Union, Tuple
from autocfg import dataclass, field
@dataclass
class MaskRCNN:
# Backbone network.
backbone = 'resnet50_v1b' # base feature network
# Final ... |
b2f6fae66bed31fa315ba74141e8764e231f551433ab9de16dd54bae13a700d4 | Python | 7,440 | 186 | import os
import numpy as np
from mirp import extract_features_and_images_generator
from mirp.extract_features_and_images import extract_features_and_images
from mirp.deep_learning_preprocessing import deep_learning_preprocessing, deep_learning_preprocessing_generator
from mirp.utilities.parallel import cluster_exist... |
0e65ba62f3175393ba67fbb47ad2c130d34b3e0196dacb372a361c2e1adb2c93 | Python | 7,442 | 202 | import numbers
import numpy as np
from scipy.linalg import eigh
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.extmath import stable_cumsum
from .utils.mean import mean_covariance
from .utils.base import sqrtm, invsqrtm
class Whitening(BaseEstimator, TransformerMixin):
"""Whitening... |
6572bf597367695b5b88aeacd9721ca9e2a96c3acef2e98a94df0be06c474172 | Python | 7,446 | 182 | """Unit tests for the creation of cross-validation folds."""
from functools import partial
import numpy as np
import pytest
from mne_rsa.folds import (
_compute_item_means,
_convert_to_one_hot,
_match_order,
create_folds,
)
from numpy.testing import assert_equal
from sklearn.model_selection import KFo... |
135e5abe79c3cda173d65f2403f9813ed43e5c1141f772fa6e371db4f82cd608 | Python | 7,447 | 136 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import json
import types
import zipfile
from pathlib import Path
import torch
from ultralytics.nn.modules import Detect
from ultralytics.utils import LOGGER
from ultralytics.utils.export.engine import _NormalizeCo... |
51366ba90dccf4879f4aae843552f20f32587c2bfa8302e6a1968a043b7e349c | Python | 7,448 | 141 | import pandas as pd
from review_comparison.generate_pred_EnzBert import get_EnzBert_predictions
from review_comparison.post_process_deepec import post_precessing_DeepEC
from review_comparison.Sequence_KNN import SequenceKNN
from review_comparison.request_to_DEEPre import Wrapper_DEEPre_server
def generate_all_predict... |
8ac19135dfa40ca8ef7582438aa446894970f1e4e92cf4cfb32913a576ac67bc | Python | 7,448 | 172 | from d2l import torch as d2l
import torch
import sklearn.metrics as metrics
from sklearn.metrics import auc, roc_curve, f1_score, precision_score
import pandas as pd
import numpy as np
from dataProcessing.modules import to_categorical
def get_accuracy(y_hat, y):
if len(y_hat.shape) > 1 and y_hat.shape[1] > 1:
... |
437c74ed48d08cd05dd55b3e8a5b4555ce20310263e48e0f88fbc9b6d1451717 | Python | 7,450 | 181 | """eigenmt.py: Re-implementation of eigenMT (Davis et al., AJHG, 2016)"""
__author__ = "Francois Aguet"
__copyright__ = "Copyright 2019, The Broad Institute"
__license__ = "BSD3"
import torch
import numpy as np
import pandas as pd
import time
import os
import sys
from collections import OrderedDict
sys.path.insert(1... |
c5e7af633e17c3ecf70f1e3b12b7d857db9ca415e66a769cdd9609744ce56eec | Python | 7,450 | 172 | import torch
from math import floor
import random
class InversionLossLayer(torch.nn.Module):
"""Loss used for most metamer generation experiments"""
def __init__(self, layer_to_invert, fake_relu=True, normalize_loss=False):
super(InversionLossLayer, self).__init__()
self.layer_to_invert = layer... |
221662919a8348b48f0dd0a2252b77f3e2c1db953ce441e4f5ca0f3db6cf1af2 | Python | 7,452 | 205 | import pytorch_lightning as pl
import torch
import numpy as np
import pandas as pd
from sksurv.metrics import integrated_brier_score, concordance_index_censored
from sksurv.util import Surv
from survival_plus_x.models.vit import vit_output_head
from survival_plus_x.losses.gensheimer import neg_log_likelihood
from sur... |
4508bd752cf4aecd2dbc938fbbc76b4508ee67fff8e01458a74ae88e12381bce | Python | 7,453 | 202 | """
This module create ProtBertProjectGOPoincareBall
"""
# pylint: disable=W0223
from curses import nonl
import logging
import torch.nn as nn
import torch
import geoopt
import numpy as np
from goatools.obo_parser import GODag
from goatools.gosubdag.gosubdag import GoSubDag
from tqdm import tqdm
import time
import torch... |
8873afed224bd7147f025d2bcf16686aef26d09a6da1e196c985943878381173 | Python | 7,454 | 213 | """F03 ledger memo items 1 + 2: canonical EVENT audit rows and sweep baseline.
Item 1's F03 slice: the tlspec-v9 ``kind="EVENT"`` audit-row WRITER (the v9
admission declared the contract; this lane lands the writer) with its
seq/prev-digest hash chain, persisting through save/load validation. Item 2:
``tl.sweep(includ... |
2e29c523e91cd140f818df71c64e959dde9f222aa24753d7623029c21583a5ba | Python | 7,455 | 191 | import logging
import os
import re
import shutil
from tempfile import TemporaryDirectory
from autouri import HTTPURL, AbsPath, AutoURI
from WDL import parse_document
logger = logging.getLogger(__name__)
class WDLParser:
RE_WDL_IMPORT = r'^\s*import\s+[\"\'](.+)[\"\']\s*'
RECURSION_DEPTH_LIMIT = 20
BASEN... |
6da91b6f6ad1554282b81cfe9152310bbb2aa76567a68065c5f39d673a443ce1 | Python | 7,457 | 197 | r"""
Boundary-Value Problems: the Gelfand-Bratu Fold
================================================
This example demonstrates PyCoBi's support for two-point boundary-value problems
(BVPs) — auto-07p's ``IPS=4`` mode. Two new ``ODESystem.from_template`` kwargs
let you express boundary and integral residuals directly ... |
3299b34202651f28cdcd068ba483e29b1b3202a2825f5eff77becbfa3338c039 | Python | 7,460 | 193 | import copy
from keras.src import layers
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.backend import KerasTensor
from keras.src.backend.common import set_keras_mask
from keras.src.quantizers.geometry import ReversibleLookupGeometry
@keras_export("keras.layers.ReversibleEmbed... |
791be238f1e44abf904eb791d8b5cb3913da005e1b2a27c1ac021b67e2f6d3f6 | Python | 7,461 | 241 | """P1 tests for the output container registry."""
from __future__ import annotations
import gc
import weakref
from dataclasses import dataclass
from pathlib import Path
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.ir.container import ContainerSpec, DictKey
from torchlens.ir.... |
23fdf6e48b52b94bef516a51c6ce6869139594761eb8d9f851da3039ec08ff0d | Python | 7,462 | 230 | """The CosmosDB/SQL backend for Celery (experimental)."""
from kombu.utils import cached_property
from kombu.utils.encoding import bytes_to_str
from kombu.utils.url import _parse_url
from celery.exceptions import ImproperlyConfigured
from celery.utils.log import get_logger
from .base import KeyValueStoreBackend
try:... |
6d8bcee09c72bd10147122b760e93236ecf98ac6659f59b1de2c34bd2d54d6be | Python | 7,462 | 169 | import logomaker
from utils import parse_config, load_CDS, build_output_dir, setup_fonts
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import os
def plot(summary_df,signed_df,window,vlim,tallest,ref,window_name,tscript,save_dir,class_type,target_pos,attr,axis=None):
... |
2c8c31643b6df0809c9d84827fd8fe8b98b5f183fae9af1da4d4df926a8d4552 | Python | 7,466 | 229 | """Sprint B1 annotation persistence and API regressions."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import numpy as np
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.data_classes.trace import Trace
from torchlens.intervention.errors i... |
41c6425ba7ae83011fa990251a4f231a90f074767a12dde841a7161e20ece76e | Python | 7,466 | 172 | import os
import json
import torch
import numpy as np
import torch.distributed as dist
from torch import nn
from model.custom_cross_entropy import CustomCrossEntropyLoss
from model.grud_model import GRUD
from model.early_stopping import EarlyStopping
from data.dataset import RegionDataset
from torch.utils.data import D... |
5a76a0124ac1a7ec39303e2b421c5840d74b76d4e36a2d597ba5b1e2e09bee6f | Python | 7,466 | 202 | """Typed refusal codes of the contrastive, depyf, nnsight and MLflow bridges.
Every refusal these bridges added raises a ``TorchLensError`` subclass that
keeps its historical built-in lineage (``ValueError``/``TypeError``/
``RuntimeError``) and carries a stable ``code`` plus a non-empty ``remedy``
(docs/reference/erro... |
58d076de9cbcbc0411549c97af1d2b176566e5c3c270696dc67f08773a8d1e4f | Python | 7,469 | 225 | """
Calibration-related plotting
"""
from __future__ import annotations
from typing import Any, Optional, Sequence
import numpy as np
import seaborn as sns
from .. import plot, reg, funcs
__all__: list[str] = [
"plot_segmentation_definition",
"plot_stride_variability",
"plot_correlated_pars",
]
def pl... |
04c2c8af24062de411fcb2a73a18c6f4f681b7617c22b933b5e25d0c103fa646 | Python | 7,470 | 203 | """Axis-permutation receptive/projective geometry battery (R20-1, fixwave-2).
Any transpose/permute/movedim between the queried operation and the model
input makes the descriptor's input-axis order differ from the unit's
output-axis order. Zipping windowed unit coordinates in descriptor order
silently TRANSPOSED exact... |
82c747f55b5869571370fd6bcd960fcb557fc14aa076f55cb01d61e0c93b446b | Python | 7,472 | 197 | import math
import hydra
import torch
import torch.nn as nn
from einops import rearrange
from flash_attn.bert_padding import index_first_axis, pad_input, unpad_input
from flash_attn.flash_blocksparse_attn_interface import (
convert_blockmask,
flash_blocksparse_attn_func,
)
class FlashBlocksparseAttention(nn... |
8cba905d5c9aa8c35f8cd802df10af6105699fbe8099a23a5ca092e9446fd69c | Python | 7,473 | 195 | """Pickle / ``tl.save`` parity for intervention-spec-carrying traces.
Pre-fix, plain ``pickle`` of a Trace captured with ``intervene=`` failed
(``zero_ablate.<locals>.factory`` and ``when.<locals>._predicate`` are local
closures) while ``tl.save`` of the same trace succeeded -- a serialization
split on one object. Two... |
4e7202b94f92d1d6e2c0a6dabab2b75c37823981ac1060b0b896c1a37d9d75ce | Python | 7,474 | 200 | import pickle
import warnings
import numpy as np
import pytest
import gym
from gym.envs.registration import EnvSpec
from gym.logger import warn
from gym.utils.env_checker import check_env, data_equivalence
from tests.envs.utils import (
all_testing_env_specs,
all_testing_initialised_envs,
assert_equals,
)... |
10ce7b1eb3ce13900129f02b1b96bf1bee8285d9e048f69094986fae123b48ec | Python | 7,476 | 214 | """
===============================================================================
Visualization of SSVEP-based BCI Classification in Tangent Space
===============================================================================
Project extended covariance matrices of SSVEP-based BCI in the tangent space,
using princi... |
49a7eefbe3178deffd60a40c6fd766b6c4ab743642d2bc7d7eaf7a8856f031c5 | Python | 7,476 | 187 | # --- 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 XBins(_BaseTraceHierarchyType):
_parent_path_str = "histogram2d"
_path_st... |
f760e195f34372da767b4e53d4bef9f4f6470afad6792c59047bcea1517813d0 | Python | 7,476 | 187 | # --- 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 YBins(_BaseTraceHierarchyType):
_parent_path_str = "histogram2d"
_path_st... |
b1812ea06657aafef1674f1557e51564b56c5946fdf53b465f60f563dee2c414 | Python | 7,477 | 225 | # 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... |
f13a654e2b69d1e34ae9611f0daab495ecc223ddf3d40ff1b4d6d864456979b8 | Python | 7,477 | 225 | import numpy as np
from neurogym.core import TrialEnv
from neurogym.utils import spaces
class DelayMatchSample(TrialEnv):
"""Delayed match-to-sample task.
A sample stimulus is shown during the sample period. The stimulus is
characterized by a one-dimensional variable, such as its orientation
between... |
7aeac59dfddfe4b37a2488f679dfbe8c935175b846cf616f71c5dc295a9e675b | Python | 7,480 | 194 | """Dual Attention Network
https://arxiv.org/abs/1809.02983"""
from mxnet.gluon import nn
from mxnet.context import cpu
from mxnet.gluon.nn import HybridBlock
from .segbase import SegBaseModel
from .fcn import _FCNHead
from .attention import PAM_Module, CAM_Module
# pylint: disable-all
__all__ = ['DANet', 'get_danet', ... |
87c4e1822c4e4b3a406cafe152b55b1fb1ed4d7c6d34881fd652baa85f8de88c | Python | 7,480 | 219 | """Visual Tracker Benchmark.
Code adapted from https://github.com/STVIR/pysot"""
import json
import os
from glob import glob
from tqdm import tqdm
from mxnet.gluon.data import dataset
from gluoncv.utils.filesystem import try_import_cv2
class Video(object):
"""
Abstract video class. get video class information... |
cacb294aedfc597c071bfe6d2c794222bc35b0741bd56a31670ace58ea3c8033 | Python | 7,480 | 274 | import locale
locale.setlocale( locale.LC_ALL, 'en_US.UTF-8' )
import re
import pandas as pd
import numpy as np
def clean_numbers_str(text):
chars = ['%', '*', '#']
if type(text) != str or text is None:
return text
for ch in chars:
text = text.replace(ch, '')
return text.strip(... |
5c686df38fba3bbfb2696991d86705105b1e8a8c9c626e9bcda41550c234729b | Python | 7,481 | 256 | """Backward observer tests for tap and record spans."""
from __future__ import annotations
import torch
from torch import nn
import torchlens as tl
from torchlens.observers import TapObserver
class _TinyRelu(nn.Module):
"""Tiny module with a paired ReLU grad_fn_handle."""
def __init__(self) -> None:
... |
a43de75ca08f093a5771a5af490d60b5f24ea5cacabb11cb7cce32b374ef0a71 | Python | 7,481 | 217 | """
===============================================================================
Visualization of SSVEP-based BCI Classification in Tangent Space
===============================================================================
Project extended covariance matrices of SSVEP-based BCI in the tangent space,
using princi... |
b682be9d8de56e1c7d34226adb008ba84a32299b3860d8ca45252a6850dd9e09 | Python | 7,481 | 238 | """Functions for generating model components."""
import numpy as np
from specparam.utils.checks import check_flat
from specparam.modes.modes import check_mode_definition
from specparam.sim.transform import rotate_spectrum
##############################################################################################... |
75cd52a079fa8e879b5e1556ade80f332498fba6b691fbffb68934e5738982b9 | Python | 7,482 | 232 | #!/usr/bin/env python
"""
User defined variables and functions that are used across all scripts.
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import (
sosfilt,
iirfilter,
# cheby1,
)
from functools import partial
from somnotate._plotting import plot_signals, plot_states
from so... |
c80f43bfc494cfd2ea11c3ff64df53ea64536cd0eb2299f15d94124f02f47283 | Python | 7,482 | 135 | """
Workflow recommendation engine using Transformer neural network
"""
import argparse
import os
import sys
import time
sys.path.append(os.getcwd())
from scripts import extract_workflow_connections
from scripts import prepare_data
from scripts import utils
import train_transformer
import train_dnn
import train_cnn
... |
aa1834e66290765f1d92a28788d822fd9af6eab3c60d7775779d78d5b2d36945 | Python | 7,483 | 198 | #!/usr/bin/env python3
# coding: utf-8
"""
Created on Jun 2020
@author: Victor Manach <victor.manach@telecom-paris.fr>
@author: Rémi Jaylet <remi.jaylet@telecom-paris.fr>
"""
from typing import Optional, Union
import numpy as np
from scipy import sparse
from scipy.spatial import cKDTree
from sknetwork.embedding.base ... |
aea205c51cb76e6cc7e7650a1e77ebcceb984119063da7da6ac685fc59e085bb | Python | 7,483 | 186 | """Script to generate keras public API in `keras/api` directory.
Usage:
Run via `./shell/api_gen.sh`.
It generates API and formats user and generated APIs.
"""
import os
import re
import shutil
import namex
PACKAGE = "keras"
BUILD_DIR_NAME = "tmp_build_dir"
def ignore_files(_, filenames):
return [f for f in ... |
eefc7b873fd1b671070e355b1414703fd763d4808691a70c7f91ef7453864b4c | Python | 7,485 | 176 | """Save-entry gate helpers for ``torchlens._io.bundle.save``.
Three entry-time guards that run before (or instead of) the per-trace save
pipeline: the two PERMANENT erasure-prevention invariants (edge-substitution
carriers and the shard-local disclosure, both keyed on the ACTIVE SCHEMA so a
regression re-fires them), ... |
075721ab0c36bd223a58775bc5d1e651f7aa70c546f7bbaa6f802299bb286573 | Python | 7,486 | 182 | #!/usr/bin/env python3
#-*-coding:utf-8-*-
# Copyright (c) 2022 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/lic... |
677b786d55b63b191b0fb1bd9e6d0b729c1352b6f93b683d52d944bde5f4e1c6 | Python | 7,486 | 266 | """
====================================================================
Augmented Covariance Matrix
====================================================================
This example compares classification pipelines based on covariance maxtrix (CM)
versus augmented covariance matrix (ACM) [1]_.
"""
# Authors: Igor Ca... |
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