sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a76b0352cd54f2ff6cc7be3af8736703306ccda0e05774a07d117de3fde169a5 | Python | 7,414 | 182 | #!/usr/bin/env python3
#
# Copyright (c) 2019 Seoul National University
#
# 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... |
fa2584a54733f0aca6d3b7b229595cd7f792f114507ecb47aa97959cf2241747 | Python | 7,416 | 252 | import pytest
import torch
from ..rno_block import RNOBlock
@pytest.mark.parametrize("n_dim", [1, 2, 3])
@pytest.mark.parametrize("complex_data", [False, True])
def test_RNOBlock_basic(n_dim, complex_data):
"""Test RNOBlock with basic functionality"""
modes = (8, 8, 8)
width = 16
size = [12] * n_dim
... |
5a0415a3ea45f382530246029db5faf4f3a83f4d326f44b2efd5d5156fbc52a2 | Python | 7,418 | 191 | '''
- Convert rule to mesh (c, v, t)
- Convert system to mesh (triangulation object)
'''
import numpy as np
import mesh.shapes as shapes
from mesh import prepare_system
## Function to convert system to Triangulation
def triangulate_system(*tria_generator_args, tria_generator=None, external_flow_field=None):
'''
... |
5512dfd6172d9c368476dfebde21f8d6b2e81d72752aeaa9cbe64b01e5ef5948 | Python | 7,422 | 176 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 agre... |
33c80fe65ca0b973085cc7045c6854351ed07c9224a276a07e51e9091a6e264f | Python | 7,423 | 210 | import torch
import torch.nn as nn
# from mmdet.core import bbox2result, bbox2roi, build_assigner, build_sampler
from ..builder import DETECTORS, build_backbone, build_head, build_neck
from .base import BaseDetector
@DETECTORS.register_module()
class TwoStageDetector(BaseDetector):
"""Base class for two-stage de... |
0e0f8e73c4f617d250170316e5b0cde88f04b09c3088b30b0325883e86462f5e | Python | 7,424 | 209 | ####################################################################################################
# Copyright (c) 2016 - 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
ff8417479efa1695c1bf9b8eb628f02f78dda1496ef46d929b2d14aadf5cc234 | Python | 7,426 | 191 | # Copyright 2020 Google Research. 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 applicable law... |
5f08c9824393ad312d166e4c1c03ad01f4f8f25bf16adcff3a1c5dc540813735 | Python | 7,428 | 136 | # Copyright (c) 2016, Konstantinos Kamnitsas
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the BSD license. See the accompanying LICENSE file
# or read the terms at https://opensource.org/licenses/BSD-3-Clause.
from __future__ import absolute_im... |
aa587b59e6aa77415865334c91cbe01b163849652ad8b991036dfa8d36159539 | Python | 7,430 | 192 | #!/usr/bin/env python
import argparse
import joblib as jl
import numpy as np
# empirical value, in range from 0 to 1;
# the higher, the more confident prediction will be
# I recommend starting from 0.8 and increase threshold
# if too many positive results are reported
# -- V. Fishman
THRESHOLD=0.8
# again, very ... |
04fa3a1a18be35a6244e7e573c4cba369447ca0ff789840099c1bfee2fbe623b | Python | 7,432 | 182 | import argparse
import os
from os import path
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import ShuffleSplit, GridSearchCV
from sklearn.metrics import (mean_absolute_error, mean_squared_erro... |
40bfb6f39d8bdd48f83ae79fa61780b6c2ab39005b5050740638eec97bf7e131 | Python | 7,435 | 214 |
import tensorflow as tf
import numpy as np
import pandas as pd
from scipy import interpolate
from .Dataset import get_network_input_obs
def linclip(i1, i2, v1, v2):
"""
Return function to calculate beta for clipped linear growth
"""
def beta(i):
a = (v2 - v1)/(i2 - i1)
b = (i2*v1 - ... |
a59d9b64de700b4a1904651df03b02912a85269da42f8327a3a52940a8ac7e5b | Python | 7,436 | 186 | # Copyright 2020 Huawei Technologies Co., Ltd
#
# 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... |
dd5c7a9c52df9b0cd303aeee31af57f34963796db7db89fc9f81074c0a55b69d | Python | 7,436 | 178 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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... |
9f80cbeaaa7ed799c17cf5fb4a8ce533b657adab583ce2ba5efd11c971f66809 | Python | 7,440 | 224 | '''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import numpy as np
import pickle
from torch.utils.data import WeightedRandomSampler, DataLoader, TensorDataset
import pandas as pd
import torch
def load_data(time_windo... |
b1693acef711eed164d932f9de682181d872249befd18d2b40a3ce780ebb7999 | Python | 7,442 | 231 | import torch
import torch.nn as nn
import math
import torch.utils.model_zoo as model_zoo
import torch.nn.functional as F
__all__ = ['ResNet', 'resnet18_plain', 'resnet34_plain', 'resnet50_plain', 'resnet101_plain',
'resnet152_plain']
model_urls = {
'resnet18': 'https://download.pytorch.org/models/resn... |
bbe1f7450c3e3196b3cb8f28dfa233b6c5bc2102e32adcc9a391ba8ed9206f03 | Python | 7,442 | 174 | #!/usr/bin/env python2
import os
import sys
import operator
def get_files_by_file_size(dirname, reverse=False):
""" Return list of file paths in directory sorted by file size """
# Get list of files
filepaths = []
for basename in os.listdir(dirname):
filename = os.path.join(dirname, basename... |
c723c769a01c1c8ee2dca7e32330eb056198ef83575afd1f8f5dee8a1fa04ac1 | Python | 7,446 | 279 | import argparse
from typing import Union
def boolean_string(s: str) -> bool:
"""helper function, turns string into boolean variable
Args:
s (str): input string
Raises:
ValueError: if s neither False nor True
Returns:
bool: s turned into boolean
"""
if s not in {"Fals... |
0cae958ea3c2942b168e157461acc8e4df12d5ef633a2738620965480e98bb7c | Python | 7,447 | 207 | """
This module provides the `ISMResult` class, which stores results for
an *in silico* mutagenesis experiment.
"""
import numpy as np
import pandas as pd
from ..sequences import Genome
class ISMResult(object):
"""
An object storing the results of an *in silico* mutagenesis
experiment.
Parameters
... |
a9a82d0170cfa85c7252eb483c4f876fdfd1c97a959299ab732e6b5dd1fa4c47 | Python | 7,449 | 181 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import pickle
from collections import OrderedDict
import torch
from maskrcnn_benchmark.utils.model_serialization import load_state_dict
from maskrcnn_benchmark.utils.registry import Registry
def _rename_basic_resnet_weights(layer... |
5ed5754c8bf559b340ef186c1955f0b8b74506b1dd78af95d02b81866362aeff | Python | 7,450 | 188 | from dash import Patch
from dash_extensions.enrich import Output, Input, State, callback, clientside_callback, no_update, ctx
from dash.exceptions import PreventUpdate
import numpy as np
def register_segment_callbacks():
# Simulate click on left- and right-arrow buttons when left- and right-arrow keys are presse... |
6846d51a82f36adbef8ebe2bf3735f2c9be2a8977df8534fcfcffae51e5a7798 | Python | 7,450 | 211 | import logging
from typing import Union
import torch
from anndata import AnnData
from scvi.core.modules._base import FCLayers
from scvi.data import transfer_anndata_setup
from scvi.core.models._utils import (
_initialize_model,
_load_saved_files,
_validate_var_names,
)
from .base import BaseModelClass
l... |
78e95b2126e67a1e3a037703baca9f19516026abcfee38483c59d1c831411429 | Python | 7,454 | 186 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 agre... |
5c7116ef3289617734c216af462a23b5034c529fcd13a9bbacf9fdcedadd06a4 | Python | 7,460 | 290 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
import linecache
import os
import re
import subprocess
import numpy as np
from tmkit.interface import Topology
from tmkit.sequence import F... |
d405201437cf6c713f3427dff7591720397cbc297c633e8f3712e76727412d48 | Python | 7,464 | 211 | import torch
import torch.nn as nn
# from mmdet.core import bbox2result, bbox2roi, build_assigner, build_sampler
from ..builder import DETECTORS, build_backbone, build_head, build_neck
from .base import BaseDetector
@DETECTORS.register_module()
class TwoStageDetector(BaseDetector):
"""Base class for two-stage de... |
c88188c1ee08fd32fb8608980e83b0ce5d180b6cc8164c69cacf8e87402d0a1f | Python | 7,468 | 176 | import tensorflow as tf
import tensorlayer as tl
import numpy as np
import os
import time
from config import config
from model import UNet_A, UNet_B
from model.util.tf_pb import save_graph_as_pb
from utils import *
n_num = config.PSF.Nnum
n_slices = config.PSF.n_slices
label = config.label
model_type = ... |
952675e307ec553125d92039c897a88c4bed8c922b9843a47fc3fa487bc2fb72 | Python | 7,469 | 226 | import torch
import numpy as np;
# Original implementation:
# https://github.com/warmspringwinds/pytorch-segmentation-detection/blob/master/pytorch_segmentation_detection/utils/flops_benchmark.py
# ---- Public functions
def add_flops_counting_methods(net_main_module):
"""Adds flops counting functions to ... |
1ad906b4565f6f2b9f9070ac762bbab929d5f881f81871fa540d1adef68d17e4 | Python | 7,472 | 190 | import numpy as np
import h5py
import matplotlib.pyplot as plt
from icecream import ic
import warnings
import pandas as pd
import seaborn as sns
warnings.filterwarnings("ignore")
def read_h5(filepath, i, o, b=48, has_mask=True):
mask = None
with h5py.File(filepath, 'r') as hf:
vx = np.asarray(hf... |
31f8e470d35f3cf223d62337917979afbfe88f322220aac68475d4f05207dd43 | Python | 7,473 | 190 | #!/usr/bin/env python3
#
# Copyright (c) 2018 Institute for Basic Science
#
# 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 u... |
e47afceb9cc9d227c60ebd53822ea096ae44d1306e15e468f772afa582d483c9 | Python | 7,477 | 239 | import copy
import random
from functools import wraps
import torch
from torch import nn
import torch.nn.functional as F
import numpy as np
from torchvision import transforms as T
from torchvision import models
from net.models.modeling import VisionTransformer, CONFIGS
# helper functions
def default(val, def_val):
... |
512d229bf43a3d919e7318a9418c6f8e4ffa9de47a4be6ef9ccaa41463b27a93 | Python | 7,480 | 202 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from maskrcnn_benchmark.modeling.box_coder import BoxCoder
from maskrcnn_benchmark.structures.bounding_box import BoxList
from maskrcnn_benchmark.structures.boxlist_ops import cat_boxlist
from maskrcnn_benchmark.structures.boxlist_ops... |
8e48145e0e773a6d07c9e40cf64989050ca5ba5de9b21ac1c0784296689c86d8 | Python | 7,480 | 195 | ######################################################################################88
FREDHUTCH_HACKS = False # silly stuff Phil added for running on Hutch servers
if FREDHUTCH_HACKS:
import os
from shutil import which
os.environ['XLA_FLAGS']='--xla_gpu_force_compilation_parallelism=1'
os.environ["T... |
6763e260460823cb46c3231200b0ab62e3037d99d3aa108b9df41905a9a6f65e | Python | 7,481 | 200 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..builder import LOSSES
from .utils import weight_reduce_loss
def cross_entropy(pred,
label,
weight=None,
reduction='mean',
avg_factor=None,
class_weight=N... |
fb1a02837f0fdb2ece22fcfc956bc57bc7a5d511724eddf8a252ed9e16214379 | Python | 7,481 | 203 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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... |
ba424c1238aea3345c7161f123de904ab4c52a808813a9e257c17e57d2e2f67a | Python | 7,483 | 187 |
from __future__ import absolute_import
import sys
import torch
import torch.nn as nn
import torch.nn.init as init
from torch.autograd import Variable
import numpy as np
from pdb import set_trace as st
from skimage import color
from IPython import embed
from . import pretrained_networks as pn
import lpips as util
de... |
0c3df97fb28df569aa5ab5e650855289e3057c203bab94549f2ee5d3467e83a6 | Python | 7,488 | 177 | """
File: cmd_line_arguments.py
Created: 2020/06/29
Last Changed: 2020/11/22
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Software Foundation, eit... |
9a8de4ee78422aac9f22eac5c563375f49d503462a36ae0cdedc9c6284e4ff8f | Python | 7,488 | 225 | #!/usr/bin/env python
import os
import subprocess
import time
from setuptools import find_packages, setup
import torch
from torch.utils.cpp_extension import (BuildExtension, CppExtension,
CUDAExtension)
def readme():
with open('README.md', encoding='utf-8') as f:
co... |
052291f93280b6ca649c3e6386e77c47e7711402aedc2bd8863fa46f1526495a | Python | 7,492 | 223 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
import numpy as np
import torchvision.models as models
from model.utils.config import cfg
from model.roi_crop.functions.roi_crop import RoICropFunction
import cv2
import pdb
import random
def save_net(fname, net):
... |
c16f4661f54c0ff49cf885b7bbc3ff53504c58e039ce6108ef8479cbfc1b91e9 | Python | 7,492 | 184 | import logging
from dataclasses import dataclass, field
from typing import Iterable, Iterator, Tuple
from oaklib import BasicOntologyInterface
from oaklib.datamodels.validation_datamodel import SeverityOptions, ValidationResult
from oaklib.datamodels.vocabulary import IS_A
from oaklib.interfaces.obograph_interface imp... |
6385130127cb88c897e21441d20d20cfc7b510ae47ea8167635eb07ac8762a50 | Python | 7,494 | 147 | """Exercise world.set_sky_light_map / clear_sky_light_map on a live server.
python skymap_test.py --port 3300 --out /path/captures [--probe hyb_illum_7c2cf6cd.jpg]
Spawns a car, looks at it from behind (so the car's left is the image's left), captures:
a) default sky, b) synthetic map (blue top / orange bottom, ... |
d91642a86d322aba447f39ff6aca7dee80d5d2a33c31b2f2dec6914582087ce5 | Python | 7,494 | 221 | import argparse
import ast
import glob
import os
import sys
import pandas as pd
import pathlib
import re
import subprocess
from collections import namedtuple
"""
Usage: python3 parse_GS_genomes.py -f <input_sample.tsv> -d <absolute path to create directories>
Parses analyses request csv from Stager for exome re-anal... |
84a19b896cdb6bc0ee57b7ef13829e532e5438e135e50c0a87404207dcb8b473 | Python | 7,495 | 202 | from defaults.paths import paths
from modules.parameters import ParameterSet, copy_dict
import numpy as np
import sys
"""
single_neuron_fI
- simulate a single neuron, driven by direct current input and determine the neuron's fI curve
- run with single_neuron_dcinput in computations
- debug with run_single_neuron_dcinp... |
ddec2d2aab76d5854aa1504e4c35e2c97dd7e2ee92b80d42bd6e85cad929f0a1 | Python | 7,497 | 177 | '''
Updated version:
Now use tangent and normal vectors in input
Use them when building the mesh, respecting flagellum material frame
Also take into account rotations of flagellum normals when calculating the velocities.
-> Works only for the case of planar beat!
'''
import numpy as np
from scipy.linalg import norm
i... |
56c8871fa2a680612a520bb42e243da3fc7ac43b3570e18102f9877c8ccdf89d | Python | 7,498 | 173 | """The viewer's video export (``carla_cosmos.viewer``) — headless, on a tiny synthetic result.
The point of the export is that it is *the viewer*, serialised: same compositor, same tiles, same
labels. So the tests decode the produced mp4 with OpenCV and compare it against what
:meth:`Composer.render` draws for the sa... |
9ad43acfefa5eb15b9de863c1aedd96db8f0e2868c8afe1d2be326515551c91e | Python | 7,499 | 182 | """
Contains code for logging approximate FID scores during training.
If you want to output ground-truth images from the training dataset, you can
run this file as a script.
"""
import os
import shutil
import torch
import copy
import argparse
from torch.utils.data import dataset
from torchvision.utils import save_ima... |
867f8419992c4e3b432247ad5d86d4649b98b6ba80a867cf84993c1f4d8d8f43 | Python | 7,501 | 191 | import tqdm
import ipdb
import argparse, sys
import random as rand
import torch
from metrics import *
from graphxai.explainers import *
from graphxai.datasets import load_ShapeGGen
from graphxai.datasets.shape_graph import ShapeGGen
from graphxai.gnn_models.node_classification.testing import GIN_3layer_basic
def get... |
515f61c9593ead35cef88edd240f8815388547760679a5ff7d853f325c337998 | Python | 7,507 | 177 | __author__ = 'duarte'
import copy
from preset import *
import numpy as np
"""
single_neuron_patterned_synaptic_input
- main spike_input stimulus processing
"""
run = 'local'
data_label = 'example2_patterned_synaptic_input'
# ############################################################################################... |
367a912dfb1b8a2355d86d41a6cc9f8dab02d12c5e2a2d1cda8135309385e167 | Python | 7,514 | 207 | #!/usr/bin/env python3
"""
File: add_gene_to_matrix.py
Created: 2020/10/20
Last Changed: 2020/10/28
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 ... |
727ed4b068d5d4363aca995c757e41951f4350ac956f370a1510a0d70b40f598 | Python | 7,514 | 189 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 agre... |
fa1fb008e2884b9c09c98d225d908d860b4e21103acd929cd2652efd5581576f | Python | 7,515 | 222 | #!/usr/bin/env python3
"""
File: visualise_single_cell_expression.py
Created: 2020/10/27
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Fr... |
af563e39f6dd7c1ad9f73c4be5785741dd7adc3656cf0272e0280a26ab8e295b | Python | 7,518 | 198 | import numpy as np
import torch
import cv2
from matplotlib import pyplot as plt
from PIL import Image
from sklearn.metrics import (confusion_matrix, f1_score,
jaccard_similarity_score, precision_recall_curve,
roc_auc_score, roc_curve)
class AverageMeter(objec... |
c4ec08edd527474e994feabadd7c584e36dc03eb1e6ff102a175bc8625d9261c | Python | 7,519 | 225 | """Several dataclasses for storing all transcript related data.
Statements are split into two varietes, embedded and speaker statements. Embedded statement appears
as part of a speaker statement. Embedded statements contain only minimal amount of information
while speaker statements can have more associated data.
Sta... |
a24985c4ab3afe8f1458cf9f5b29d55f7285ed8ea7c4bc934c26a40e10babaed | Python | 7,520 | 189 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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... |
44c234ce954c3dc1848680faffcc60e8e897aca0d089426f77ee2bf6fb7d2e73 | Python | 7,521 | 203 | """
Shared code to run a sequence-like experiment where cells are driven by random background activity
and one or more cells are forced to spike at fixed times.
"""
import logging
import pandas as pd
import numpy as np
from tqdm.auto import tqdm as pbar
from tctx.util.profiling import log_time
from tctx.util import si... |
242b745653be0ec77520ea0c5ba532122bad71c1bc3485584bfcc9f9e4cb0607 | Python | 7,523 | 210 | # Copyright 2020 Huawei Technologies Co., Ltd
#
# 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... |
ce889deb1b15b72d5b57fc347697debaeb892b83413fec9e1eb6a92ce5367321 | Python | 7,523 | 210 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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... |
2e42f16040fa7f6126c0730e27225d673f4c94df69b72af2e4766b58bb95f356 | Python | 7,524 | 222 | #//=============================================================
#//Copyright (c) 2011 G. Gogoshin
#//Distributed under MIT-style license.
#//(see LICENSE.txt or visit http://opensource.org/licenses/MIT)
#//=============================================================
import numpy as np
import csv
import oflib
def ... |
96d43e966d5f931b3f777a2a18dd0075768c3f569782865800ab8d94ed85adbf | Python | 7,524 | 225 | import warnings
import torch
import torch.nn as nn
from torchnlp.nn import Attention
from blitz.modules import BayesianConv1d, BayesianLinear
from blitz.utils import variational_estimator
class LinearDropRelu(nn.Module):
def __init__(self, in_features, out_features, dropout=0, bias=True):
super(LinearDro... |
7263088f1e3726a90c9e9e429857188242b562e8c1df6537c17e6ab4f5b3a10f | Python | 7,525 | 227 | from collections import defaultdict
import pytorch_lightning as pl
from torchmetrics import MeanAbsoluteError as MAE
from torchmetrics.classification import MulticlassF1Score as F1
import torch.nn as nn
import torch
from functools import partial
from ..layers.diverse import MLP, AlphaPredictor
from ..layers.features_in... |
26a4006194d85e82afb288693c827f60908ec44a456da47daedc4688cc5c0e16 | Python | 7,533 | 244 | import os
from typing import Iterable, List
import numpy as np
import torch
from cgtasknet.tasks.reduce import (
CtxDMTaskParameters,
DMTaskParameters,
DMTaskRandomModParameters,
GoDlTaskParameters,
GoDlTaskRandomModParameters,
GoRtTaskParameters,
GoRtTaskRandomModParameters,
GoTaskPara... |
890d0c20740b90dcb6fd4799b5fe187b121ab4f5d4ed6c506de7e3e49c9ac031 | Python | 7,534 | 203 | import os
import torch
import yaml
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from glob import glob
from torchvision.transforms import Compose
from torch.utils.data import DataLoader
from timeit import default_timer as timer
from dataset.SamplePadder import SamplePadder
from dataset.SampleStan... |
907984dfbcb918b07c119500ef485ead1e29942a9b929f51ebcb74f3b48cf288 | Python | 7,534 | 197 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# 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... |
f5876d1dcca8d08787aea7d7a816792ec71874dce96adfad7a14c6dd427a3f6c | Python | 7,534 | 247 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Variational Animal Motion Embedding 1.0-alpha Toolbox
© K. Luxem & P. Bauer, Department of Cellular Neuroscience
Leibniz Institute for Neurobiology, Magdeburg, Germany
https://github.com/LINCellularNeuroscience/VAME
Licensed under GNU General Public License v3.0
"""
... |
f351f97b73537fbed8ca29b886b690f9f86a7d1e6f4aaf167a0f26549ef4fd47 | Python | 7,539 | 183 | ####################################################################################################
# Copyright (c) 2019, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free softwar... |
7ddfcc489adb57c1fce0586b085a71ba0a58c1c8406df3472723a437b9c6a3f9 | Python | 7,541 | 167 | import os
import numpy as np
import sys
import time
import torch
import torch.nn.functional as F
from torchvision import transforms
import torch.nn.init as init
import random
import pandas as pd
from itertools import chain
from skimage.io import imread, imshow, concatenate_images
from skimage.transform import resize
f... |
f1b990e03acb1b39c1c2edd78bb89f7a16cd3e70779da38322c9e0152e9c4731 | Python | 7,541 | 259 | # %%
import os
from pathlib import Path
import colorcet as cc
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from matplotlib.collections import LineCollection
from matplotlib.lines import Line2D
from sklearn.decomposition import PCA
from umap import UMAP
fro... |
30afda1e5bc068310d8e92de804b1fec7ca25054b6e42bd4deddc08c09c558e7 | Python | 7,542 | 230 | import os
import time
import logging
import multiprocessing
import pickle
import gzip
import bz2
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
import umap.umap_ as umap
import numpy as np
import pandas as pd
from pathlib import Path
from sklearn.model_selection import ... |
684a218886fb3bc1857112d41dc7a5977266f4ec6cbf7cd73df94fbcd1e9e7fe | Python | 7,542 | 218 | import nibabel as nib
import os.path as op
import os
import numpy as np
import logging
import pimms
from AFQ.tasks.decorators import as_file
from AFQ.tasks.utils import with_name, str_to_desc
import AFQ.data.fetch as afd
from AFQ.utils.path import drop_extension, write_json
from AFQ.definitions.mapping import SynMap
f... |
fd54b2b5f1f0234fde35525d4b8191b5d9093612161d7e54cdf54a8c81136d1d | Python | 7,543 | 182 | #!/usr/bin/env python3
"""
File: export_decon_to_excel.py
Created: 2021/02/16
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Software ... |
1ebef4c602bc52db4bdecfdbfec773a72b04168a9b64170d5131d0c23d6d9a14 | Python | 7,544 | 216 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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 Software Foundation, either version 3 of... |
9a1782c74684aa3e8137d02a681aa53a76c0b575b7fd93e53ea3e0c06d1f5c9d | Python | 7,545 | 247 | import os
from typing import Iterable, List
import numpy as np
import torch
from cgtasknet.tasks.reduce import (
CtxDMTaskParameters,
DMTaskParameters,
DMTaskRandomModParameters,
GoDlTaskParameters,
GoDlTaskRandomModParameters,
GoRtTaskParameters,
GoRtTaskRandomModParameters,
GoTaskPara... |
53e695e5007bd7dfdce73ee7f298269ff139cc9043bb71639274ed4e9d739fb7 | Python | 7,546 | 175 | import logging
import shutil
import unittest
from oaklib.datamodels import obograph
from oaklib.datamodels.search_datamodel import SearchTermSyntax, SearchProperty
from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.... |
ee0b808e19a9948e34f247d1b1d368b24cc1b29181a9a7812539b0cf2b6b8ffd | Python | 7,546 | 144 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 agre... |
984ef965e5f9154daa7cc40df013d8cd427dd4e9f77f8e6168232a000b8a695c | Python | 7,548 | 202 | #!/usr/bin/env python3
"""Accelerator coverage scan for LAMMPS pair styles.
Lists every base pair style with the accelerator variants it has (OPENMP, GPU,
KOKKOS, INTEL, OPT), how many force-style YAML references exercise it, how many
example and benchmark inputs use it, the size of its implementation, and a few
struc... |
ab77eab3bd9c36e7d7a189b5e16f5afce55b05994e1950a2121bba9a2d3eedb7 | Python | 7,548 | 248 | import os, time, random
from numpy.core.fromnumeric import size
from numpy.lib.type_check import imag
from tqdm import tqdm
from skimage.transform import resize # not using, highly inefficient
from skimage.util import montage
from sklearn.model_selection import KFold
import nibabel as nib
import numpy as np
from tor... |
ea34bb3fa2cc93c121ab04aa2d7e607c9113b0326292b8cdf7c2af6030377c0c | Python | 7,550 | 247 | import os
from typing import Iterable, List
import numpy as np
import torch
from cgtasknet.tasks.reduce import (
CtxDMTaskParameters,
DMTaskParameters,
DMTaskRandomModParameters,
GoDlTaskParameters,
GoDlTaskRandomModParameters,
GoRtTaskParameters,
GoRtTaskRandomModParameters,
GoTaskPara... |
17080ade9c9a0130739dc52fe09bb09fbce28ce4e77cf6ac86d6dc9e732845a9 | Python | 7,551 | 243 | """
This file contains primitives for multi-gpu communication.
This is useful when doing distributed training.
"""
import pickle
import time
import torch
import torch.distributed as dist
def get_world_size():
if not dist.is_available():
return 1
if not dist.is_initialized():
return 1
ret... |
6224bb8a914958c2278b35ba20379f84708d9e953446faa0230ba68f149502da | Python | 7,552 | 188 | #!/usr/bin/env python
# plot_tripseq_transcript.py
# plot the indicated transcript or gene based input polysome sequencing (TrIPseq) data
# Intended to be applied to fractionated polysome sequencing data (a la tripseq) but theoretically can work for any data involving transcript-specific distributions
# Input form... |
324e3c42267e95d375f101ffd124b0ce209e14a0efaeb16d03184f745b67e018 | Python | 7,561 | 132 | __author__ = 'duarte'
from modules.parameters import ParameterSet, ParameterSpace, extract_nestvalid_dict
from modules.input_architect import EncodingLayer
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.analysis import sin... |
0d10d4c5b4b11416e6c0d3ae4c0551cc3d69d2ffb2cb680e57f52367fccaafa5 | Python | 7,566 | 155 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
import os
import argparse
import torch
from src.loader import load_images, DataSampler
from src.utils import initialize_exp, b... |
c7f5b1635dc8574e2895d817c6b94eab0d1186b63516cb26c3d01b52e4c0e848 | Python | 7,566 | 257 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from itertools import chain
from .._exceptions import DefinitionError
from .._text import enumeration, plural
from .._utils.parse import find_variables
class CodeBase:
_sep = ' '
def __init__(
self,
string: str,
cod... |
b982653fc1a2dcddbad457c60462fba833a368023f876d378f8cb1319f2214bd | Python | 7,567 | 239 | '''
One-dimensional ring (`get_neighbours_list`) or chain (`get_neigbhours_list_non_periodic`) of oscillators.
'''
import math
import numpy as np
from scipy.linalg import norm
from carpet.various import mod2pi
def get_domain_size(N, a):
return N * a
def get_nodes_and_ids(num_cilia, a, direction):
direction ... |
2ef190815ce18953c775048a624f3e66b9dc47ef4a8f58c5af10f36c48969631 | Python | 7,569 | 204 | import glob
import random
import os
import numpy as np
import torch
from torch.utils.data import Dataset
from PIL import Image
import torchvision.transforms as transforms
import torchvision.transforms.functional as TF
import random
import albumentations as A
import cv2
class an_BrainDataset(Dataset):
def __init__... |
caa0fefbc500957906afabf86ac26fc3ca5a58befe6b620ef4e649742812fe4f | Python | 7,569 | 256 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from M2TR.utils.registries import MODEL_REGISTRY
'''
MODEL:
MODEL_NAME: Xception
PRETRAINED: imagenet
ESCAPE: ''
'''
class SeparableConv2d(nn.Module):
def __init__(
self,
in_channels,
out_channels,
... |
d929547d1a22abdbaca51ee51cafe0f94d202cb5d202a7ede98de44219111845 | Python | 7,569 | 209 | import os, gc
import scanpy as sc
import anndata
import numpy as np
import pandas as pd
## Plots
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import seaborn as sns
adata1 = anndata.read_h5ad('D30.h5')
adata2 = anndata.read_h5ad('D52.h5')
adata = anndata.... |
5814cf391d9faa972fbf34e0c71a8c01ed4b305259aa78343a0ac95110fff4ad | Python | 7,572 | 199 | import numpy as np
import scipy.interpolate as sc
from icecream import ic
import time
import os
from random import shuffle
import h5py
import multi_slice_viewer as msv
from scipy.spatial import Delaunay
from scipy.spatial import KDTree
from h5functions import save_to_h5
class CFDResult():
def __init__(self, filep... |
7f91c14969144aa7e6d2c50f499a80f2f3b57611ff813a1cd872315938ff5840 | Python | 7,572 | 197 | """Eelbrain GUIs"""
def run(block=False):
"""Hand over command to the GUI (quit the GUI to return to the terminal)
Parameters
----------
block : bool
Block the Terminal even if the GUI is capable of being run in parallel.
Control returns to the Terminal when the user quits the GUI app... |
35273053d12c10b4bd33f9c064d649b83d71d1a513123267c8a2fbe25d045821 | Python | 7,577 | 183 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 agre... |
88ace4af08b9f818154b61026ccf42a4275dbbbf198a7e933458e7c0f9b29c81 | Python | 7,578 | 130 | __author__ = 'duarte'
from modules.parameters import ParameterSet, ParameterSpace, extract_nestvalid_dict
from modules.input_architect import EncodingLayer
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.analysis import sin... |
afb690cf4ce07f26451ea8b8a90099e9db623c126a8622e014868093c1fdc17b | Python | 7,578 | 206 | from torchmetrics.functional import confusion_matrix
from pytorch_lightning.callbacks import Callback
from .network_tools import is_concerned
from collections import defaultdict
from tqdm import tqdm
from ..data.datamodule import EMPTY_FIELD_VALUE
import os, sys
import torch
import numpy as np
import matplotlib.pyplot ... |
b289552ad0894077c837a68e7b4f5a802ee4c9b37ebbf170cce4ac70080750d7 | Python | 7,578 | 268 | import torch.nn as nn
import torch
import numpy as np
from torch_geometric.nn import GlobalAttention, global_mean_pool
from ..data.data_tools import edges_geom_causal
from torch_sparse import SparseTensor
from torch_geometric.data import Batch
from torch.nn.utils import weight_norm
## Basic perceptron
class ExpLayer... |
7a37e1a1152790dc1687541396e2931761f403e8ea11814d4881edc982f40a7d | Python | 7,579 | 214 | import tqdm
import networkx
import numpy as np
from rdkit import Chem, DataStructs
from rdkit.Chem.Fraggle import FraggleSim
from rdkit.Chem import Descriptors as rdFMCS
from drugex.utils.fingerprints import get_fingerprint
from drugex.training.scorers.interfaces import Scorer
class TverskyFingerprintSimilarity(Sc... |
4bd5e2a5424f87d3aba1bb7de5ad39a4d8e9eba88a9a94ab88733a75d628167e | Python | 7,586 | 187 | from ..transforms.data_processors import DefaultDataProcessor
try:
from einops import rearrange
except ModuleNotFoundError:
print(
"Trying to import data processors for TheWell without required dependency\
``einops``. Run ``pip install einops`` and try again."
)
raise ModuleNotFoundEr... |
7de74103801ab85e9f909dfe2386f3fcbc53a08a5b8466da147ab37be866c20d | Python | 7,591 | 156 | # Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and rel... |
a3c9261cd5f0911b992d5103140e6159d06c34335d8d10fb29d3d93a0fe2ab4b | Python | 7,595 | 218 | '''
https://github.com/akaraspt/deepsleepnet
Copyright 2017 Akara Supratak and Hao Dong. All rights reserved.
'''
import argparse
import glob
import math
import ntpath
import os
import shutil
from datetime import datetime
import numpy as np
import pandas as pd
from mne.io import concatenate_raws... |
ba77b63863c911a292083c2bc577d2987654678a187b5ca215db35d1486dd1a4 | Python | 7,595 | 227 | '''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import numpy as np
import pandas as pd
import torch
def load_data(time_window, config, data_type, clinicalBERT, embedding_type):
imputation = 'imputed'
... |
dcd1d32e988fb71c3524c3b7c790ea7749d2599d7a305ed50701d63905c86b1a | Python | 7,596 | 201 | import logging
from abc import ABC
from enum import Enum
from typing import Iterable, List, Optional
from pydantic import BaseModel
from oaklib.datamodels.vocabulary import IS_A
from oaklib.interfaces import MappingProviderInterface, OboGraphInterface
from oaklib.interfaces.association_provider_interface import Assoc... |
6e89cf3401a04a7b470f7d37aafd2ccd98ac32a06382605bef6598bffa6b7e57 | Python | 7,597 | 214 | # Modified from https://github.com/facebookresearch/detectron2/tree/master/projects/PointRend # noqa
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.modules.utils import _pair
def normalize(grid):
"""Normalize input grid from [-1, 1] to [0, 1]
Args:
grid (Tensor): Th... |
a920b88a603a14b3368cf2796b0940d182e21a75cb72ae32154240a6b0033548 | Python | 7,597 | 197 | import torch
from torch import nn
from .conv_ws import ConvAWS2d
from .registry import CONV_LAYERS
import torch.nn.functional as F
class Flatten(nn.Module):
def forward(self, x):
return x.view(x.size(0), -1)
@CONV_LAYERS.register_module('MDConv')
class MDconv(ConvAWS2d):
def __init__(self,
... |
a7daadfe46885b0941576c96abc9fe8633f62a4c124d4b715b4eba409940ff58 | Python | 7,600 | 160 | import argparse
import os.path as op
from glob import glob
import numpy as np
import pandas as pd
def _get_parser():
parser = argparse.ArgumentParser(description="Get subjects to download")
parser.add_argument(
"--dset",
dest="dset",
required=True,
help="Path to BIDS directory... |
4f0c7b184a694ea41d07a9a0d8e9d80eedc2f047def0b21d49d88b77e3a8384e | Python | 7,604 | 171 | # Copyright 2017 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
#
# 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
#... |
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