sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
369585a526a8c03e6c60adb044c92a7231adef0e3f1d414b6ec35103c26ccedc | Python | 6,552 | 152 | import os
import json
from urllib.parse import quote, unquote
import numpy as np
from typing import Iterator, Dict, Union
import pandas as pd
from torcheeg.datasets.module.base_dataset import BaseDataset
from .base_model_selection import BaseModelSelection
from .utils import create_subset, read_indices, write_indic... |
d44053b776a3fa7b1597beb44f0b15b77062829d96aaddd6b776d533202c98f2 | Python | 6,552 | 144 | import sys
import pandas as pd
import matplotlib.pyplot as plt
import netplotbrain as npb
from scipy.io import loadmat
import statsmodels.api as sm
from matplotlib.colors import LinearSegmentedColormap
sys.path.append('/m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/src/visualization')
fr... |
0f0631709e6218326fa25f61ec09bc70e733d8f1d192971df3459a50282d355b | Python | 6,553 | 199 | # -*- coding: utf-8 -*-
import tempfile, os, pytest
import tensorflow as tf
import numpy as np
import pinn
from shutil import rmtree
@pytest.mark.forked
def test_potential_model():
"""A simple example to test training and using a potential"""
from ase import Atoms
from ase.calculators.lj import LennardJo... |
28218ac7b162e15c260a9d006bdfcde04da77a3b100c4808dfeed0b52fca99ad | Python | 6,553 | 163 | import torch
from torch import nn
import timm
class LateFusionBackbone(nn.Module):
"""
image_architecture: Architecture used in the image branch. ResNet, RegNet and ConvNext are supported
lidar_architecture: Architecture used in the lidar branch. ResNet, RegNet and ConvNext are supported
use_velocity: ... |
ee3c3d5d279e400e4af87e08e5ae74df82acda0910aa6e333d78eb8709cfd52e | Python | 6,556 | 223 | import logging
import mimetypes
import os
import pathlib
from typing import Callable, Iterable, Optional, Tuple
from pip._internal.models.candidate import InstallationCandidate
from pip._internal.models.link import Link
from pip._internal.utils.urls import path_to_url, url_to_path
from pip._internal.vcs import is_url
... |
d310410aa58e2fab4af2bdd347633afcd2e410e5a2fef7e3fb0983b638678d25 | Python | 6,558 | 138 | # This script create masks from annotations.
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning) # Ignore all FutureWarning warnings that might flood the console log
warnings.simplefilter(action='ignore', category=DeprecationWarning) # Ignore all DeprecationWarning warnings that might fl... |
f748bb79a2029026eb801a1b5e69a79a766d836de32a9a3fa55f2b933332cfad | Python | 6,558 | 184 | from __future__ import division, print_function
import copy
import numpy as np
from soundsig.incrowd import ConvolutionalInCrowdModel, fast_conv, fast_conv_grouped
class ConvolutionalLinearModel(ConvolutionalInCrowdModel):
"""
Wrapper class for use with ThresholdGradientDescent optimization class, also
... |
225db954def4651f08af18719e26e8ca2a85264744a89bf3cb9a48dd980928c0 | Python | 6,559 | 218 | import numpy as np
from torchvision import transforms
from PIL import Image
import numbers
import torch
class ResizeImage():
def __init__(self, size):
if isinstance(size, int):
self.size = (int(size), int(size))
else:
self.size = size
def __call__(self, img):
th, tw = self.siz... |
fa50133341bc90fb6704adf456e63050ee74b8561328b4b639eea30d389da53e | Python | 6,560 | 202 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
from keras.layers import Input, Dropout, Dense, Activation, LeakyReLU, Conv2D
from keras.layers import Lambda, Flatten
from keras.models import Model
from ke... |
b55c24cab5eac02da14c308420e97af9118d853da39f3df09900210c803eebb5 | Python | 6,561 | 104 | """Built-in components: the reference LiquidAion configuration, registered like any plugin.
Factories receive a context object; the fields per category are documented in docs/PLUGINS.md.
"""
from __future__ import annotations
from typing import Any
from .connectomes import cue_group, flywire_cx512, random_control_co... |
0ea06e646068044f2f39a0778fbfcbfbd88578ca00624feaec149afa1140518d | Python | 6,563 | 81 | from argparse import ArgumentParser
import numpy as np
def get_param():
parser = ArgumentParser('recon_GCAMP')
parser.add_argument('--fold_res', type=str, default='../results',help='folder in which the res will be saved')
parser.add_argument('--gpu', type=int, default=0, help='gpu index, -1 for cpu')
pa... |
3789d1825d63b5e165807997f423f067ebfc86a4b18bf2d49708953ec78b1bdd | Python | 6,563 | 163 | import math
import torch
from torch import Tensor
from typing import List, Optional
from torch.optim.optimizer import Optimizer
def adam(params: List[Tensor],
grads: List[Tensor],
exp_avgs: List[Tensor],
exp_avg_sqs: List[Tensor],
max_exp_avg_sqs: List[Tensor],
state_steps... |
df05d814e9721f65c43944a570645ea80814785456716c7f6a35b9aed9bfac3a | Python | 6,563 | 221 | import tempfile
from pathlib import Path
import pytest
import torch
from torch import nn
from elasticai.creator.nn.integer.linear.linear import Linear
from elasticai.creator.nn.integer.quant_utils.calculate_quant_params import (
calculate_asymmetric_quant_params,
)
from elasticai.creator.nn.integer.relu.relu impo... |
59b15774fbd91f27684a2e5df6eee9ddff9882a7a42b06db867aa7f0c4154b57 | Python | 6,564 | 175 | # -*- coding: utf-8 -*-
from __future__ import print_function
import errno
import logging
import os.path
import subprocess
import sys
from . import call
from . import limits
from . import portfolio_runner
from . import returncodes
from . import util
from .plan_manager import PlanManager
#TODO: We might want to turn... |
10337326f7ddddbc35198b510abe228337e87f9cfec6e17f91e1bd91a9a01288 | Python | 6,565 | 114 | from codex.configuration import MIN_SYN_THRESHOLD
from codex.data.structured_search_filters import (
STRUCTURED_SEARCH_UNARY_OPERATORS,
STRUCTURED_SEARCH_BINARY_OPERATORS,
STRUCTURED_SEARCH_NARY_OPERATORS,
STRUCTURED_SEARCH_ATTRIBUTES,
SEARCH_ATTRIBUTE_NAMES,
)
def operators_list(ops):
def _ma... |
ec10f70fc61e1b4ab6ddf3a2864d0696e52aded8546778ae849e804f7a1f01db | Python | 6,566 | 164 | # import time
#
# import torch
# import torch.nn.functional as F # noqa
# from torch.dataloaders.preprocessing import DataLoader
# from torch.optim.lr_scheduler import ExponentialLR
# from torch.optim import Optimizer
# from torch.dataloaders.tensorboard import SummaryWriter
#
#
# def train_epoch(model: torch.nn.Modul... |
261fba59ee4028e1970ba50b6a8ffeeda8034923ec4e2b6a81fa8aaedeeec4df | Python | 6,567 | 161 | """A worker result that lands DURING teardown must not rebuild the tab.
``_process_template_path`` starts a metadata worker whose GUI-thread result
handler calls ``_refresh_preview_template``, which starts ANOTHER QThread and
touches widgets. If that result is delivered while the tab is being torn down,
it create... |
d39b9a20f3b39c93d0ed5811766182986e2c0e750fb7082fe6a39822a6cbd946 | Python | 6,567 | 217 | # actions.py
from .exceptions import ParseException
from .util import col, replaced_by_pep8
class OnlyOnce:
"""
Wrapper for parse actions, to ensure they are only called once.
"""
def __init__(self, method_call):
from .core import _trim_arity
self.callable = _trim_arity(method_call)... |
52d86d5aa87a1771376b2ae1e0ccb3085537f232bca66dd00fe95e64c37d60d5 | Python | 6,568 | 151 | import numpy as np
import os
import pandas as pd
import torch
import torchvision
from tqdm import tqdm
from constants import CLASSIFICATION_LABELS, N_ITEMS
from src.dataloaders.semantic_transforms_dataloader import get_dataloader
from src.utils import class_to_score
class SemanticMultilabelEvaluator:
def __init_... |
b54f18d8a9692fb4cf2902c298169099b0f703f93257b30b0d67b24ac7535604 | Python | 6,568 | 232 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
8565a2dbeca8b04458bbde369e47dbb9aee23434c9e38457705a62d3d97be27b | Python | 6,569 | 188 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
3119a5416fecd78d3ad3d099d97ea5a1b4c029d288e817ec62af972650eebb0c | Python | 6,571 | 162 | # -*- coding: utf-8 -*-
import tensorflow as tf
from tfsnippet import Distribution, Normal
class RecurrentDistribution(Distribution):
"""
A multi-variable distribution integrated with recurrent structure.
"""
@property
def dtype(self):
return self._dtype
@property
def is_continuo... |
bc6f224ec182f9f7022f1ebd4b5bbf2e666de309a10357c1940b0514c322c694 | Python | 6,571 | 138 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
"""
import numpy as np
import os
from pathlib import Path
i... |
95b8d8ec69eb553273c76e4e3a4776681f9a90b96c633d794bd33edd31703bb9 | Python | 6,572 | 149 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : sdmatrix.py
# Author : Yufeng Liu
# Date : 2023-01-30
# Description :
#
#======================... |
d798ad6bc191954ed0e765912e05b0f0f7b7cdafe06adb6c2f45a80574cfbdec | Python | 6,572 | 200 | # -*- coding: utf-8 -*-
"""
Created on Wed May 3 18:52:51 2023
@author: Dustin Garner
"""
"""
-----------
Maintenance
-----------
maintenance.find_undone_input()
================
#Last Run 5/8/23, identified 9 neurons.
maintenance.check_joined_concurrence(all_mt_l + all_mt_r + tb_l + tb_r + \
... |
c25935b93a3eab8311871d109d5ce0119d0ce14cd1fb6940fb9a0ddf16994a66 | Python | 6,573 | 221 | """
Functions for command line interface to generate cluster / peak summary
"""
import argparse
import os.path as op
from atlasreader.atlasreader import (
_ATLASES,
check_atlases,
create_output,
read_atlas_peak,
)
def _check_limit(num, limits=[0, 100]):
"""
Ensures that `num` is within provi... |
4bd5db8f7b6704fcb680ac6526a01db9c76e7c4093e001fa3cbb4e6ca1d455dc | Python | 6,575 | 210 | import torch
import torch.nn as nn
import numpy as np
import math
from torch import nn, Tensor
class PositionalEncoder(nn.Module):
def __init__(self, dropout=0.1, max_seq_len: int=5000, d_model: int=512, batch_first: bool=True):
super().__init__()
self.d_model = d_model
self.dropo... |
e9de12d8918089299867f1cf1778dc86a396990a64cc50277124acf4052afbc1 | Python | 6,576 | 202 | import pytest
import numpy as np
from pupil_recording_interface.device import BaseDevice
from pupil_recording_interface.device.video import (
BaseVideoDevice,
VideoDeviceUVC,
)
from pupil_recording_interface.device.flir import VideoDeviceFLIR
from pupil_recording_interface.device.realsense import RealSenseDevi... |
61e94378ca1dd29cf3e30ccf2ed7412cca5febcbf2b42835b19019204f28b011 | Python | 6,579 | 185 | """The scale-consistency verdict has to reach a human.
The check runs on every section and costs roughly a quarter of the batch. All of that is
wasted if the result stops inside the worker - and it did: ``MaskingWorker.run`` built its
summary dict field by field and simply omitted ``suspect``, so every pipeline-le... |
dc0a4c12fdd532604cdc378b716b1402b29dfb6ab3cd08b472eaf4dd3029f33a | Python | 6,579 | 143 | from tqdm import tqdm
import torch
import torch.nn as nn
from captum.attr import (
IntegratedGradients,
LayerConductance,
)
import warnings
warnings.filterwarnings("ignore")
from dataset import MicroDataset
from model import MicroKPNN_MTL
def explain_meta_to_disease(model, wrapped_model4disease, batch, device):... |
475c4d452c7dbfc510d50ff4d5a383d35113f6e82f10cb8c9c0d6e8339edf951 | Python | 6,580 | 227 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
fc6ba6c7895926c203ded9afa53019cfb54957fdea205682ed270307f5147a05 | Python | 6,580 | 161 | #! /usr/bin/env python
USAGE = """\
Update baseline:
* change BASELINE variable below
* push the change
* login to computer running the buildslave as the buildslave user
* remove ~/experiments dir
* run in an updated repo (e.g. in ~/lib/downward):
export PYTHONPATH=~/lib/python/lab
export DOWNWARD_CO... |
70522be328216b39216b592692c1a3332cb9b2311485e41529a7944c65c067e5 | Python | 6,581 | 166 | import glob
import os
from os import listdir
from os.path import isfile, join
from pathlib import Path
import numpy as np
from uptake import make_data_folder
import scipy.signal
def define_pkl_filename(particle, mechanics):
"""
Args:
params: class of imput parameters
Returns:
... |
829b825e90d5df6e19cfb877788848beaae4052d58dd886d16c61df5073de7ff | Python | 6,581 | 172 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
792ac0770c73bd305ac87f7ad7ec66bd51ab7a2a01bd42b9cc7b1bd0a6bf0509 | Python | 6,584 | 167 | import torch
import torch.nn as nn
import torch.nn.functional as F
class GraphConvolution(nn.Module):
def __init__(self, in_channels: int, out_channels: int, bias: bool=False):
super(GraphConvolution, self).__init__()
self.in_channels = in_channels
self.out_channels = out_channels
... |
089c513c939b16a5cb07c7ace11fef58c00a588f9a8eb90c2abf227f1e8b5be0 | Python | 6,586 | 168 | from collections import defaultdict
import csv
from logging import Logger
import os
import sys
from typing import Callable, Dict, List, Tuple
import numpy as np
import pandas as pd
from .run_training import run_training
from chemprop.args import TrainArgs
from chemprop.constants import TEST_SCORES_FILE_NAME, TRAIN_LO... |
613bc15f36a31e5a74c97165bda4d76d9c90736548b1c8e4c6971eb81de9036b | Python | 6,586 | 245 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
9145725cef9d1e22d72539d8eae557484149744d70a8536c245e37c57a938221 | Python | 6,587 | 174 | # Node group "Principal Components" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are reg... |
dfabebfc105417de9213ccf4476d6b212f89a9424760302f29339254cec50cd9 | Python | 6,588 | 226 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
01e19692ec27e341842a2284687ea8e4771f4c93c187b938289ed2982e5de1c6 | Python | 6,589 | 143 | import numpy as np
from .bgwio import bgw_vsc
from .lcaodata import LCAOData
from .utils import slice_same, tqdm_mpi_tofile
from .matlcao import pairs_to_indices, indices_to_pairs, MatLCAO
from .gridintg import GridPoints
'''
This module implements several functions needed by real-space construction of AO Hamiltonian... |
1a05cd0d06ad1a09bbef45b2855e13ca463ade277c58866d91bc2c328a02ffda | Python | 6,589 | 172 | """
Train a DARNet Model on the DTU Dataset
=======================================
In this tutorial, we'll walk through how to leverage TorchEEG for training a DARNet Model to classify auditory attention using the DTU dataset. Let's walk through the essential steps—from dataset preparation to model evaluation.
"""
... |
0a90f99e1e76f531fe9ccd901d3d042b1492b1056499f11a47923725143068ce | Python | 6,590 | 189 | #!/usr/bin/env python
from __future__ import print_function
import numpy as np
import random
from itertools import combinations
from collections import namedtuple
from copy import deepcopy
from examples.continuous_tamp.primitives import get_pose_gen, inverse_kin_fn, get_region_test, plan_motion, \
tight, blocke... |
01eb04203fb880f143593c0f88f68666e0f8b70753fa299a1ae311e597d29fcb | Python | 6,591 | 199 | import importlib.resources
import locale
import logging
import os
import sys
from optparse import Values
from types import ModuleType
from typing import Any, Dict, List, Optional
import pip._vendor
from pip._vendor.certifi import where
from pip._vendor.packaging.version import parse as parse_version
from pip._interna... |
1ed9009f8d2d862179d907d2f18a95b70f5d6e5c0c2f3d5c859689f98738ed1a | Python | 6,591 | 218 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
51651484bb09a5aab705fc0544abf4b6853e9de3c71948580d9494882d1dfaa4 | Python | 6,591 | 212 | """DICOM format loader (.dcm) for volume_io."""
from __future__ import annotations
import gc
import os
from pathlib import Path
from typing import List
import numpy as np
try:
import pydicom
_HAS_PYDICOM = True
except ImportError:
_HAS_PYDICOM = False
# nibabel is optional - only nee... |
accc502ba20d7c0c3e63c3e8a61cd28030cf3c8cc57b868b470be2ca1f6fde58 | Python | 6,591 | 161 | # -*- coding: utf-8 -*-
"""
Created on Tuesday August 4th 2022
@author: Pablo Maceira Elvira
Logistic regression is used for binary classification. However, predictions can be interpreted as a probability, as
the sigmoid (i.e., the logistic function) is bounded between 0 and 1. Ultimately, what I want is to be... |
eb8f3f6670533020cacbe45ca718bb77533d90170de59dca336496921507273d | Python | 6,592 | 185 | # -*- coding: utf-8 -*-
"""
Created on 15 october 2023
@author: divyoj
"""
## importing libraries:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# # note that this must be executed before 'import numba'
# os.environ[... |
806ff15e20f82f686b07e6c73ffc8ae0ef04b4e9ba1ab38905f3d8949a7736b7 | Python | 6,594 | 266 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
d17c99e16ee91a3a352950c391c52465254364f2878b4031a85f21ba78756d26 | Python | 6,595 | 158 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : sdmatrix.py
# Author : Yufeng Liu
# Date : 2023-01-30
# Description :
#
#======================... |
06700b2295e8c083b87338379e2c802541f113d0357b5aa3b78456f09ea169ef | Python | 6,596 | 200 | import sys
import argparse
import os
script = os.path.basename(sys.argv[0])
nArgs=len(sys.argv)
if nArgs < 2:
aid=script+' takes YourFile.csv (or YourFile.zip) of rowsXcols numbers\n\t ' + \
'and produces a UMAP result in YourFile.umap.csv'
else:
print('script arguments: '+ " ".join(sys.argv[1:]))
... |
074fac8c8d6330bde566987d0b8cf34fc3919641f960d4bbf19005c8cd84734f | Python | 6,596 | 170 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
2cead72e02340a3425743a36ce1399606619ea0e1efdc24e081fe917d68c4564 | Python | 6,596 | 184 | from __future__ import annotations
import ctypes
import os
import sys
from functools import lru_cache
from typing import Callable
from .api import PlatformDirsABC
class Windows(PlatformDirsABC):
"""`MSDN on where to store app data files
<http://support.microsoft.com/default.aspx?scid=kb;en-us;310294#XSLTH31... |
91ce4f234ce0fe711011fac27a937138fc9e6a38d0050f187b6d395547a7ea9e | Python | 6,598 | 282 | import unittest
from parameterized import parameterized
from tests.utils import Utils
from HyDGL.tools import Tools
class TestTools(unittest.TestCase):
@parameterized.expand([
[
2,
0,
[1, 0]
],
[
2,
1,
[0, 1]
... |
bfd976322bdaef6d13867d8b0440c634e2efc0334edf0f5377b636af47d4e5da | Python | 6,599 | 227 |
device = '0'
name = ''
import os
os.environ['CUDA_VISIBLE_DEVICES'] = device
from stephenHeadConfig import conf as conf
import PoseUMDN
import tensorflow as tf
import PoseTools
import math
import PoseUNet
import cv2
import PoseCommon
mov = '/home/mayank/Dropbox (HHMI)/temp/stephen/C002H001S0001_c_2.avi'
out = '/ho... |
24cb1172fb407f3f718f87291a978ac0f677857025abc113e9d5a79fc5f043f4 | Python | 6,601 | 175 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
fd261711e2b398357fe91d24db80c64c06ac93a092d1af100ba72bf90ab2a785 | Python | 6,604 | 150 | import torch
from tqdm import tqdm
from base import BaseTrainer
from .tracker import MetricTracker
class Multi_DNN_Trainer(BaseTrainer):
'''
Multi DNN Trainer
'''
def __init__(self, config, train_data_loader, valid_data_loader=None, test_data_loader=None):
'''
Initialize the Multi DNN... |
d7d5b476b6ecb5424a8290def850a0c67f18a88eef1216d11228fa5ef9dfe91c | Python | 6,606 | 200 | import torch
import torch.nn as nn
from torch.nn.modules.loss import _Loss
from torch.distributions.distribution import Distribution
from torch.distributions.kl import kl_divergence
# NOTE Here we are defining losses for minimization, so essentially we negate the
# log-likelihood or the ELBO.
class ReconstructionLo... |
0814e9109e9608d19a4f1d4ffe7eddef943fd0af2aad96f452dc83fc921334f5 | Python | 6,607 | 128 | """
This script summarizes the significant results for global efficiency, participation
coefficients, and selected links, organizing them and matching the results with
the node coordinates for H3
"""
import os
import pandas as pd
###############################################################################
# Change... |
24a2b42d2b70feed920f49db25406be18daff458d7f578349f2824e608d0f137 | Python | 6,607 | 169 | from codex.data.vocabulary import STOP_WORDS
from codex import logger
from codex.utils.parsing import tokenize, edit_distance
class SearchIndex(object):
def __init__(self, texts_labels_id_tuples):
self.CS_label_to_row_id = {}
self.ci_label_to_row_id = {}
self.CS_token_to_row_id = {}
... |
77cb9a5c345c41231d863ddeb065f630c8b448be0f017567d2697a9da1798434 | Python | 6,607 | 198 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
78c4ed8d6b117b96c1101a26f3bce5a896089691d554b8ac190cff6e7e4903e8 | Python | 6,608 | 153 | import os
import re
from copy import copy
from typing import List, Tuple, Union, Dict
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
class KFoldGroupbyTrial:
r'''
A tool class for k-fold cross-validations, to divide the training set and t... |
00a75b668b891fbdae97827881e360ffa5bb651f0ed993ece831f6fcba4252ec | Python | 6,610 | 207 | """
Generate the "Color PyMOL", "Color VMD" and "Color CSS" nodes from the named
colours that `molecularnodes.color.parse_color` reads.
uv run docs/dev/named_color_nodes.py
uv run -m nodebpy.assets build && uv run -m nodebpy.assets dump
PyMOL and VMD colours come from `molecularnodes/_color_names.py`, CSS col... |
9faedb9d69df60ef325909d0efa230a175aada0d8035823b32bd955fca4e35fb | Python | 6,610 | 96 | from nipype.pipeline.engine import Workflow, Node
from nipype import DataGrabber, DataSink, IdentityInterface
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.spm as spm
import nipype.interfaces.matlab as mlab
import os
from nipype.interfaces.utility import Function... |
5d862ff7a346ff9864874608a46808cad504cd19ecc3e4a3ed723ec4d178fce3 | Python | 6,611 | 170 | from typing import Any, Callable, List, Optional, Type
import torch
from torch import nn, Tensor
from ..modules.residuals import InvertedResidual, Conv2dNormActivation, Block
def _make_divisible(v: float, divisor: int, min_value: Optional[int] = None) -> int:
"""
This function is taken from the original tf r... |
596334201287c2d77dafa97208678ca8d69a79e41aaaea91bfc7b79ed42a9a44 | Python | 6,612 | 205 | import json
import os.path
import random
import dash_bootstrap_components as dbc
import dash_renderjson
import openai
from dash import html, get_app, register_page, Input, Output, State, dcc, ctx
random.seed(42)
def get_completion(prompt):
prompt += "\n\n###\n\n"
inference = openai.Completion.create(
... |
b627469c7ea77f762259feaaf0bd92a2742fba229333fa7e0fdbf230d175779e | Python | 6,613 | 186 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
def conv3x3(in_planes, out_planes, stride=1):
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride, padding=1, bias=False)
class BasicBlock(nn.Module):
expansion = 1
def __init__(self... |
828d949799f72dcbd45177e374704f5581523261b725b159a4f1bc6819a1db74 | Python | 6,614 | 176 | import ast
import glob
import logging
import os
from typing import Dict, Optional
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.init as init
from dataLoader.NextXVisit import NextVisit
from sklearn.metrics import average_precision_score, roc_auc_score, recall_score, f1_score... |
83ae0329a7b268b0fee54ed8e051341b92a3e5a302f5c2accb48a17e0e011bcc | Python | 6,614 | 191 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2024 Clinic for Diagnositic and Interventional Radiology, University Hospital Bonn, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy ... |
15b27d134781c155077f821795037b9cec22475bf4951d8a661296dd692d79fc | Python | 6,615 | 129 | import csv
import itertools
import json
import uuid
from unittest.mock import MagicMock
import pytest
from NDATools.upload.cli import ValidatedFile
from NDATools.upload.validation.api import ValidationV2Credentials, ValidationV2
from NDATools.upload.validation.results_writer import JsonWriter as JsonValidationFileWri... |
55c3f114ed15c53b964156bffa7eef8fa5781a3672b3848e638971f249511e89 | Python | 6,616 | 167 | import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from typing import Any, Dict, Optional
from models.model import Model
class He3DCNN_Net(nn.Module):
"""
MULTI-SCALE 3D DEEP CONVOLUTIONAL NEURAL NETWORK FOR HYPERSPECTRAL
IMAGE CLASSIFICATION
Mingyi He, Bo Li, Huahui C... |
56b3c27509c5fa1be296fa212ac6594fffde9f8d0fc793b086fb46f363e832a8 | Python | 6,616 | 149 | import copy
import os
import unittest
from hed import schema
from hed.models import HedString
class Test(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.base_data_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../data/")
cls.hed_schema = schema.load_schema_version(... |
5a261446194abe997ad3ba3e52033b57df87d06d2786b681123fc4f8b689aed4 | Python | 6,616 | 185 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
''' Script to compute evoked responses and their inverse solution '''
# Append paths
proj_name = 'MINDLAB2020_MEG-AuditoryPatternRecognition'
wdir = '/projects/' + proj_name + '/scratch/working_memory/'
scripts_dir = '/projects/' + proj_name + '/scripts/working_memory/'
i... |
a3eabb792c191ed142818d67dc9bfac4b694fba8517364ee5e6137f0052b0829 | Python | 6,616 | 234 | #!/usr/bin/env python
import gzip
import os
import subprocess
import sys
from datetime import datetime
from shutil import which
import pysam
def run_shell_cmd(cmd):
"""
Execute a command on bash shell with subprocess.
"""
p = subprocess.Popen(
["/bin/bash", "-o", "pipefail"],
stdin=s... |
d633f0c683ec262983d232f4ab030fb910304ea82383f639376a54deb64b3c9b | Python | 6,616 | 198 | from __future__ import annotations
# built-in
import json
from collections import defaultdict
from copy import deepcopy
from importlib import import_module
from pathlib import Path
from typing import Any, Callable, Sequence
LIBRARIES_PATH = Path(__file__).parent / 'libraries.json'
class LibrariesManager:
libs:... |
0bab78dd4a2bcaf929c1945af2070414f9ad43465ce4a97d2ae11564b99f83de | Python | 6,617 | 177 | import matplotlib.pyplot as plt
import numpy as np
from IPython import embed
def clean_transfer_data(region, comp, comp2, group):
with open(f"txtfiles/avg_transfer_{region}_{comp}_{comp2}_{group}.txt", 'r') as infile:
lines = infile.readlines()
filename = f"avg_transfer_{region}_{comp}_{comp2}_{gr... |
9496002d21fdb4af6fa47e8b84244e3529a439dae6435852d06fb2bd68a44c9f | Python | 6,617 | 152 | ############
# https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer
# This code was taken from the repo above and was not created by me (Fabian)! Full credit goes to the original authors
############
import math
import torch
from torch.optim.optimizer import Optimizer
class Ranger(Optimizer):
... |
93923a4bb6c55bb14b50d6d42567d469c7dc1a6ad1f46fee02655006c634145c | Python | 6,620 | 174 | import cv2
import numpy as np
import os
import pandas as pd
import shutil
from skimage.color import rgb2gray as skimage_rgb2gray
from skimage import io
from tqdm import tqdm
from typing import *
from constants import *
_DATA_ROOT = '/Users/maurice/phd/src/rey-figure/data/'
_TEX_REPORTS_ROOT = os.path.join(ROOT_DIR, '... |
b0fc6afd9e8442eda1701c6bda45cb4f335ae2604153dc669dcf6ee6ee164e31 | Python | 6,620 | 182 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
32ecf9221b544b579271f24c76bf5b7daec1617227f7b60f4e935130aaad56bd | Python | 6,621 | 171 | import argparse
from datetime import datetime
import json
import time
import os
import ramanspy as rp
import unmix
def run(
scene_sizes,
scene_type,
num_endmembers,
spectral_size,
*,
replicates,
training_epochs,
noise=False,
baseline=False,
... |
eb2248728a02e0407368a4a25391655f965e25cd84dcfa37962e8e0bc25763f1 | Python | 6,623 | 156 | import numpy as np
import torch
from torch.nn import Linear as Lin, Sequential as Seq
import torch_geometric as tg
import torch.nn.functional as F
from torch import nn
from PAE import PAE
from layers import general_GCN_layer, snowball_layer,truncated_krylov_layer
class graph_convolutional_network(nn.Module):
def _... |
8a28d0fe324e268f4529dc6ca1bba1b3b511f35bb2d3cf55b51c0523e6916c77 | Python | 6,624 | 146 |
extensions = dict(
required_params=['training_frame', ('cols', "NULL")],
validate_required_params="",
set_required_params="""
parms$training_frame <- training_frame
if(!missing(cols))
parms$ignored_columns <- .verify_datacols(training_frame, cols)$cols_ignore
""",
set_params="""
# Check if user_y i... |
50f3840c8cce400ee35e570186fbb192f149ee615a8edc1eec15133ee5cf7120 | Python | 6,625 | 168 | """ Code for neuropixel analysis (output kilosort/phy2) """
# look script_dualPhase3-2.m from http://data.cortexlab.net/dualPhase3/data/script_dualPhase3.m
# Also time is ok as Marie says: -1 sec at beginning (- 1 at the end)
import numpy as np
import pandas as pd
from pathlib import Path
import os.path
import pdb
i... |
5429d0ac4f2491ec0a6d04650210ac1371361cfd2d4e8f6793ae2d5a5f4ef451 | Python | 6,626 | 162 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import cProfile
import pstats
import random
import numpy as np
from examples.continuous_tamp.optimizer.optimizer import cfree_motion_fn, get_optimize_fn
from examples.continuous_tamp.primitives import get_pose_gen, collision_test, distance_f... |
54d9a034970bd5a8bef4d5f7353b11665ed42d3b468e2ba329f0bff2726b82bc | Python | 6,626 | 193 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
aff1380d7db5dc5515a58dfdecf41fe1de43b9f96649b834952032b12ce662a1 | Python | 6,627 | 163 | """The --atlas CLI choice list is sourced from the live ATLAS_REGISTRY, so every
registered atlas (BBP, DevCCF, Paxinos, ... not just the original three) is
selectable, while a typo is still rejected rather than silently falling back to
Allen CCF (get_atlas returns _ALLEN_CCF for unknown names)."""
import os
imp... |
a0d33661dfb3655bb9ae5c896811576f0daef34027bf1850ba215684b5fd9b8c | Python | 6,628 | 169 | from sklearn.decomposition import PCA
import numpy as np
import scipy.signal as signal
import pandas as pd
def compute_wavelets(x, actual_sr, n_wavelets, C_min, C_max, morlet_w):
## Computation following Sakamoto
# Morlet wavlet by scipy: exp(1j*w*x/s) * exp(-0.5*(x/s)**2) * pi**(-0.25) * sqrt(1/s)
# not... |
a42729d3ae91bcc6da68887641e009eac6515ef1960cad921c5ffcedb99177bd | Python | 6,628 | 224 | import numpy as np
from tqdm import tqdm
import networkx as nx
import scipy.sparse as sp
import random
from time import time
from collections import defaultdict
import pickle
import warnings
# from imblearn.over_sampling import SMOTE
warnings.filterwarnings('ignore')
from os import error
import numpy as np
import pand... |
eeef36bb2e705df6f92812057d67f04958c67dc091dc1f10f3dc081a047903f0 | Python | 6,628 | 189 | """ Pipeline for preprocessing EEG data.
Prodecure includes the following steps:
- Load raw data
- Remove bad channels
- Set reference and eog channels
- Anti-alias filter at 1/3 of the goal frequency
- Notch filter to remove power line noise
- Segment data while accounting for delay
- Decimate data to the goal freque... |
9c1d56a9df84bfd12b6e6702f02e79eba2232700289cf21db902c0c0bc8fad8e | Python | 6,629 | 198 | import numpy as np
import pandas as pd
from scipy.ndimage import gaussian_filter
from src.file_handling import fname, load_tiff, write_tiff, save_params_json
from src.visualization import (
plot_corr_heatmap,
plot_ccf,
plot_aligned,
plot_corrmap,
save_dual_movie,
save_img,
)
from src.processing... |
0d29074d440ba2b7d211100a13fa1300450579f667669e1b41be2af2b1db2b0b | Python | 6,630 | 225 | import sys
import time
from typing import TYPE_CHECKING, Callable, Dict, Iterable, List, Union
if sys.version_info >= (3, 8):
from typing import Final
else:
from pip._vendor.typing_extensions import Final # pragma: no cover
from .segment import ControlCode, ControlType, Segment
if TYPE_CHECKING:
from .c... |
2d9eeb19d46aab1fa4ed5b093b800be1a09802ee0931245d00413c30fd5755bb | Python | 6,631 | 156 | # Node-group asset "Evaluate on Atoms" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHEC... |
9d75c8738c8a3e4335d8dde9e4d98656df0eadd501d3aea60814fe15c43e2c45 | Python | 6,631 | 226 | from collections.abc import Callable
import pytest
import elasticai.creator.function_dispatch as FD
from elasticai.creator import ir
from elasticai.creator.ir2vhdl import DataGraph, Shape, factory
from elasticai.creator_plugins.grouped_filter import FilterParameters
from elasticai.creator_plugins.time_multiplexed_seq... |
bb9680453024ef36be161c44184ffc9e9a44361075838698f23a546743d8d52c | Python | 6,632 | 200 | from typing import Optional, Callable, Tuple
import torch
import torch.nn as nn
from src.models.utils import conv_block, fc_layer
__all__ = ['get_reyclassifier']
class ReyClassifier2(nn.Module):
"""
binary classifier, designed to predict whether or not a given item is present in the rey figure
"""
... |
f3e63c9af8d25bfc54f88d7acd0861d177c32d279441dd3929d09a0540959018 | Python | 6,632 | 175 | """
Superimpose one molecule onto another.
The fit is done with biotite on the atoms in Å, in each molecule's own local
frame, and applied to the mobile molecule's Blender object as its world matrix.
The coordinates themselves are left untouched, so the alignment can be undone,
moved by hand afterwards and survives tr... |
fc8c7a4d3c18bbac85b3579d0cae640c522813a5d74ee4cb9628b37100a1adc8 | Python | 6,632 | 198 | from pathlib import Path
import numpy as np
import torch
from torch import nn
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.MPQ.matrixmulti import MatrixMulti
from elasticai.creator.nn.integer.MPQ.scaleddotproductattention.design import (
Scal... |
ff3ba4f19a4aff1ddf696bdd7a9972d16cbc4630a7fe08addfbb1837938f29de | Python | 6,633 | 205 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
61037b15e1dc041950e11c2bba16279e3983295ae1b428a79e31e64e57120d09 | Python | 6,636 | 186 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
9e714d8dc471e01453580934d5f61a49e20e5d1c4bac50a4502a4ee000aaa461 | Python | 6,636 | 254 | """Utility functions for dealing with dictionaries."""
from __future__ import annotations
import logging
from collections.abc import MutableMapping
from copy import deepcopy
from pathlib import Path
from typing import TYPE_CHECKING
from monty.json import jsanitize
from monty.serialization import dumpfn
from quacc.w... |
2c89c6814ed7a6e0116e0a6e3f2c2a1f6acb9f06d261bdb65f085972dc694953 | Python | 6,640 | 173 | # Import necessary libraries
import os
import torch
import numpy as np
import matplotlib.pyplot as plt
from PIL import Image
import imageio # Import imageio for GIF creation
# Enable automatic casting for mixed precision training with CUDA
torch.autocast(device_type="cuda", dtype=torch.bfloat16).__enter__()
# Check ... |
cbc32b121b14822ac569b38c44b11be1cbe0f3aa882dc33066220e2839bd1055 | Python | 6,641 | 150 | import os
import re
from copy import copy
from typing import Dict, Tuple, Union
import numpy as np
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
class KFoldCrossTrial:
r'''
A tool class for k-fold cross-validations, to divide the trainin... |
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