sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
99ffb34ce94a493b5c52e8846951787aecb1857c63d9da95771819438197e2d9 | Python | 4,458 | 120 | """Functions for processing and visualization.
This module contains mandatory functions to run different preprocessing / postprocessing steps on input fMRI
images."""
import numpy as np
import operator
import torch.nn as nn
from typing import Tuple, Union
from nilearn.masking import unmask, apply_mask
from nibabel.n... |
a4c29bda552b23027dc1fb3bd6a6d6592bc00f8f9320528c6152b4913c3b74f8 | Python | 4,458 | 130 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
inspect_simulation.py
---------------------
Script to plot simulated network activity of
2D rate model of motor cortex, see paper
Kang, Ranft & Hakim. eLife (2023).
To load specific simulation output change parameters/
filename accordingly.
Created March 2023
Auth... |
d2c3d10e173ca79fd0180664b7d98a079656317bf864188cb42b5d42f5b6f37b | Python | 4,458 | 130 | import matplotlib as mpl; mpl.use('Agg')
from matplotlib import pyplot as plt
from matplotlib import lines as mlines
import numpy as np
import pandas as pd
from scipy import stats
def evidence(h,q,ylast):
n = ( (1-h) * np.exp(ylast) + h )
d = ( h * np.exp(ylast) + (1-h) )
y = np.log( q ) + np.log( n / d )... |
d82922cd230d1f7fe789df4da385d80c945cbafb191b71e37c548c48fe7a02c3 | Python | 4,458 | 123 | import torch
from norse.torch.functional.lif import LIFState
from norse.torch.functional.lif_adex import LIFAdExState
# from norse.torch.functional.lif_adex_refrac import LIFAdExRefracState
from norse.torch.functional.lif_refrac import LIFRefracState
from norse.torch.functional.lsnn import LSNNState
class InitialSta... |
97377624d56f6bba2a1370e6920976ae32bf62b6e01515345192bc404e15d63a | Python | 4,460 | 129 | import os, sys
import argparse, random
import numpy as np
import torch
from tqdm import tqdm
from utils import get_model, get_exp_method, get_dataset
from graphxai.datasets import Benzene
from graphxai.explainers import PGExplainer
from graphxai.utils.performance.load_exp import exp_exists_graph
from graphxai.metrics... |
23618a0c83c2916db2115c0cbf7c1084bc149dd04c48fadae6f4fddff5fc4b96 | Python | 4,461 | 114 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 29 15:32:08 2021
@author: tonifuc3m
"""
import argparse
import warnings
import pandas as pd
import os
import compute_metrics
from utils import load_entities_dict, prepro_relations, \
format_relations, get_chemical_gene_combinations, filter_pre... |
146f8a35f81dad7e4a03ad24a2d20a2f337b616c801a4e99fdc143ca609a284d | Python | 4,462 | 94 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'
import numpy as np
import tensorflow as tf
from tensorflow.keras.callbacks i... |
0757f94734deb0e51ad47cfd72c9ac545ffbf2786897fc04e966b45460c31026 | Python | 4,465 | 101 | # 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... |
188f5972fe3d322c03258b1dd5baecc933e93704d065e217f1746f9c1b6fe110 | Python | 4,466 | 140 | # Copyright 2019 The TensorFlow Authors, Pavel Yakubovskiy. 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 ... |
504d52a03f23b891aadf76e26f9c7e4c771fe5aacc68e9d4874a5451ab15e300 | Python | 4,466 | 113 | from collections import defaultdict
import logging
from typing import Dict, List
from .predict import predict
from chemprop.data import MoleculeDataLoader, StandardScaler
from chemprop.models import MoleculeModel
from chemprop.utils import get_metric_func
def evaluate_predictions(preds: List[List[float]],
... |
e413a8b534e4c3426a2e9c23ba0157d494760c80f3b980fad6ca930707ede7ab | Python | 4,466 | 135 | import os
from scipy.ndimage.measurements import label
from tqdm import tqdm
import torch.nn as nn
import torch
import matplotlib.pyplot as plt
from sklearn.metrics import accuracy_score
from sklearn.metrics import precision_score
from sklearn.metrics import recall_score
from sklearn.metrics import f1_score
... |
7a376f6c35e06c1f6a5a39421b70bed1f16a932035747829f8af8a92c4f9e91f | Python | 4,467 | 127 | # 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... |
00022c4621b27c3420513b02dccce064c8571d1ee1807ad9c9bd086b3cd9cd0f | Python | 4,468 | 125 | import torch
from torch import nn
class KeypointPostProcessor(nn.Module):
def __init__(self, keypointer=None):
super(KeypointPostProcessor, self).__init__()
self.keypointer = keypointer
def forward(self, x, boxes):
mask_prob = x
scores = None
if self.keypointer:
... |
a270b173002147a49316a1a55302b3323ab95a6541211d0946876d854b721b3d | Python | 4,469 | 100 | from typing import Tuple
import numpy as np
from scipy.linalg import solve_banded
from .sim import SimGrid
from .typing import Shape, Size, Spacing, Optional, Union, Size3
class BPM(SimGrid):
def __init__(self, size: Size, spacing: Spacing, eps: Union[float, np.ndarray] = 1,
wavelength: float =... |
d277f66858b73519961832c64da67ecaa44352ad060607e2ee6a88791ff30c64 | Python | 4,469 | 155 | import os
import numpy as np
import warnings
import sys
from numpy.testing import assert_array_equal, assert_equal, assert_raises
from bruker2nifti._getters import get_stack_direction_from_VisuCorePosition
def test_get_stack_direction_from_VisuCorePosition_OK_dummy_multiple_cases():
visu_core_position_ = np.arr... |
f65d5ac88062ae9d17408b849a3ceb7cc12c0b05a2387db0404e6be355042135 | Python | 4,470 | 127 | #!/usr/bin/env python3
"""
File: search_dataframe.py
Created: 2020/07/16
Last Changed: 2020/07/17
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 So... |
145c363a5ea5bfac8e2a36a844a6b20e24ca6ff6a9db8c7c197c39e0bae99179 | Python | 4,471 | 93 | import torch
from mmcv.runner import OptimizerHook
from mmdet.core.utils.dist_utils import allreduce_grads
from collections import OrderedDict
import torch.distributed as dist
from torch._utils import (_flatten_dense_tensors, _unflatten_dense_tensors,
_take_tensors)
class ArchOptimizerHook(... |
52fb9fc9b35ec795494bb8b03ea2360efa4aa959901f34d3573a0c822677e44f | Python | 4,471 | 133 | """
corpus
Created by: Martin Sicho
On: 26.04.22, 16:47
"""
from rdkit import Chem
from drugex.logs import logger
from drugex.data.corpus.interfaces import Corpus
from drugex.data.corpus.vocabulary import VocSmiles, VocGraph
class SequenceCorpus(Corpus):
"""
A `Corpus` to encode molecules for the sequence-b... |
f74cc205b67d36ed00e62c2829cce0cf045f6892cc02776740a5b01cb3b1d97a | Python | 4,471 | 135 | """
Copyright (c) 2019, National Institute of Informatics
All rights reserved.
Author: Huy H. Nguyen
-----------------------------------------------------
Script for testing segmentation of ClassNSeg (the proposed method)
"""
import os
import torch
import numpy as np
import torch.utils.data
import torchvision.datasets... |
b4932708e14af527f32be23978610bb20d09f252214d73930e863de733ed9911 | Python | 4,472 | 130 | # making rmats jobs directly from bam files, don't need to convert cram to bam like original
import argparse
import glob
import os
parser = argparse.ArgumentParser(description='Generate rMATs files.')
parser.add_argument('output_directory', help='Outputdir to write results to')
parser.add_argument('jobs_directory', he... |
2c0bbb50f45d5e2432caea2505f93299f39d2667e4859975d9808a4bdd7430b1 | Python | 4,473 | 128 | # 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 ... |
4bd2c9f47ae6d48bea5c5db2433d77b6f6c0442d16ea21eb37241a657cd40064 | Python | 4,473 | 144 | #!/usr/bin/env python3
# encoding: utf-8
# @Time : 2017/12/16 下午8:41
# @Author : yuchangqian
# @Contact : changqian_yu@163.com
# @File : BaseDataset.py
import os
import time
import cv2
import torch
import numpy as np
import torch.utils.data as data
class BaseDataset(data.Dataset):
def __init__(self, sett... |
7a278bdd85a564f4cbfa89b7bb83ef1d79eb42d572357f50ed551f9ff7df6cb0 | Python | 4,473 | 86 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
# WMH Segmentation workflow
# ==========================
#
# Exmple Usage:
# =============
# from wmhpypes.workflows import ibbmTum_wf
# from nipype.pipeline.engine import Workflow,... |
e4a1d71c78534db242e96388bdf5afcd3913c6e794e27cd3f678213c146ee25b | Python | 4,474 | 108 | # 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... |
7f4d87a3d99eceeae46ca24adf0bb7f7a480083991abe9cb614b496b16e7c435 | Python | 4,478 | 121 | """Phase 2: AIF agent on the same CS+/CS- conditioning task as the RPE baseline.
Same substrate (Winding connectome PN->KC wiring), same task, same seed.
Plots a head-to-head comparison: MBON readout (m_hat) and DAN signal,
RPE vs AIF, for CS+ and CS- across trials.
Expected results:
- Both models acquire CS+ cor... |
9e10bf0a592e19e5814502f54eb29f77e0b8d3a8f2ea0c342ed2317a85839d1a | Python | 4,480 | 128 | # 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... |
dd332d370bd86b9a9ef3d34c5e03097b1a05e7b18d6e551b34060cd7db954f3a | Python | 4,480 | 83 | """Render lidar / semantic lidar / radar captures of gallery.py into doc images."""
import json, math, os, sys
import numpy as np
from PIL import Image, ImageDraw
import matplotlib; matplotlib.use("Agg")
import matplotlib.pyplot as plt
D = sys.argv[1]; OUT = sys.argv[2]
meta = json.load(open(os.path.join(D, "meta.json"... |
a9f30864d34f4f2c9dc2825771d2f34bf9472c5c21a40c3ec4ff441504ad580d | Python | 4,484 | 154 | import os
import ssl
import pytest
import requests
def pytest_addoption(parser):
parser.addoption(
"--skipintegration", action="store_true", default=False, help="Skip integration tests."
)
@pytest.fixture
def skip_integration(request):
return request.config.getoption("--skipintegration")
def ... |
dfdbfa09ff72cc6e8f60bb1f8e26724c775c2df70e4a8a0d919198880bb0887c | Python | 4,485 | 119 | import os
from os.path import join
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_error,
... |
93a9519756a38ce7cb7e460a7f82349d1da9466b2f5f485969f0ed5e9f416837 | Python | 4,487 | 162 | __author__ = 'jieqing jiao'
__email__ = "jieqing.jiao@gmail.com"
import numpy as np
from scipy.interpolate import interp1d
import matplotlib.pyplot as plt
def dt2mft(dt):
mft = np.mean(dt, axis=0)
return mft
def dt2tdur(dt):
tdur = dt[1, ] - dt[0, ]
return tdur
def mft2tdur(mft):
# print('min... |
7c4b6310df2fcc98fa042b5afd07e7f160e11dfdc3690fad54107cbaefe80f7b | Python | 4,489 | 96 | import tensorflow as tf
import numpy as np
from Utilities import cdist_tf_batch, A
KC = 1389.35457644382
permutation_mask = np.array([-1., 1., 1., 1., -1., -1., -1., -1., -1., -1., -1., -1., -1.])
mask = []
for x in range(3):
for y in range(3):
for z in range(3):
base = np.zeros((3))
... |
9105e84e016aa71ce8e588b81d1e6b907191441e33da119e392481bdc034315d | Python | 4,489 | 108 | #!/usr/bin/env python3
"""
File: translate_sample_ids.py
Created: 2021/11/25
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 F... |
e6f3cfe870b1ebb6b2a0d94def47c426c78fcaed8dce3478ba64c8e7e8ec2f8c | Python | 4,490 | 130 | #!/usr/bin/env python3
"""
File: eqtl_iterations_plot.py
Created: 2020/04/27
Last Changed: 2020/04/28
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 Fre... |
d278310d1f0bd7d4a54b60e3bd073c7ed7849975c9b7562dda72d71dec60934e | Python | 4,492 | 122 | from utils.ArticlesProvider import ArticlesProvider
from utils.decomposition import Decomposition
from utils import Config
import torch
import spacy
import ftfy
import re
import json
from transformer.model_pytorch import TransformerModel, load_openai_pretrained_model, DEFAULT_CONFIG
class TransformerDecomposition(Deco... |
043cf90ee92310d2d7f28f15134b17971f35c5860cd9b8d8e661daa706977f0b | Python | 4,498 | 101 | import argparse
import torch
import torch.nn as nn
import numpy as np
import os
import pickle
from data_loader import get_loader
from build_vocab import Vocabulary
from model import EncoderCNN, DecoderRNN
from torch.nn.utils.rnn import pack_padded_sequence
from torchvision import transforms
# Device configuration
de... |
c278afa310bb6a0fc3ad34dd288b26f7d21af8449dacd7c69d2dd2190c3b7e6e | Python | 4,501 | 146 | """Labeling mitochondria and neurons by compartment (axonal, dendritic, somatic)"""
from collections import Counter
import numpy as np
import pandas as pd
from scipy.spatial import KDTree
from scipy.sparse import csgraph
import h5py
from . import skel
from . import u
ENGLISHLABELS = {
0: "Somatic", 1: "Axonal",... |
89aefe34ce212aa9a8e5d837482a61987efef20ce901cfc57f3f16ed0bded1f6 | Python | 4,503 | 189 | # %% [markdown]
# ##
from src.hierarchy import signal_flow
from src.data import load_metagraph
from src.visualization import matrixplot
from src.visualization import CLASS_COLOR_DICT
from src.io import savefig
import os
from src.graph import preprocess
import numpy as np
import pandas as pd
import matplotlib.pyplot as... |
d1fc6be06ef00952c39510b1eddcf0f4533189ffa5378c68bcf605887baaf753 | Python | 4,507 | 116 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import numpy as np
from numpy.testing import assert_equal, assert_array_equal
import pytest
from eelbrain import datasets, Celltable, testnd
from eelbrain._stats import t_contrast
from eelbrain._stats.stats import t_1samp
from eelbrain._stats.t_contrast import T... |
6ad9148c975d9d94f6bc87e4072dc150af3ddf7a12fc27b2af010d559a4c7252 | Python | 4,510 | 132 | # correlateCLIP.py
# 11/23/14
# correlates RT stops from two CLIP files (*noBlacklist_noRepeat.bed)
# uses RT stop maker from FAST-iCLIP
import csv, sys, collections, glob, os
csv.register_dialect("textdialect", delimiter='\t')
def separateStrands(mappedReads):
# Usage: separate positive and negative strand... |
8a7dc6f6c09c78f586caca7aa3a032ffdd4c9726cf0ce3c3ea56264da1b13b7d | Python | 4,510 | 154 | import os
import torch
import pandas as pd
import torchtext
import clip
import pickle
import torchvision.transforms.functional as tvf
from functools import partial
from torchvision.datasets.folder import default_loader
from torch.utils.data import Dataset
class CelebAHQ(Dataset):
base_folder = "celebahq"
im... |
12836a074266b9ce6f0cff16c6262e8552a162442842d01ae1a3a6b23c749a78 | Python | 4,512 | 116 | # Copyright 2021-2022 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... |
8ab25c290259f1cd4412591059cde414d0f29213a747b6d9004338cf47220325 | Python | 4,513 | 125 | import os
import glob
import torch
import random
from PIL import Image
from torch.utils import data
from torchvision import transforms as T
class data_prefetcher():
def __init__(self, loader):
self.loader = loader
self.dataiter = iter(loader)
self.stream = torch.cuda.Stream()
self.m... |
9b4c11e48c24cb1f901b872ef11d647d593630a6a5391147a3d0a849016c3d03 | Python | 4,514 | 120 | # Copyright (c) Open-MMLab. All rights reserved.
import copy
from torch.nn.utils import clip_grad
from ..fp16_utils import allreduce_grads, wrap_fp16_model
from .hook import HOOKS, Hook
@HOOKS.register_module()
class OptimizerHook(Hook):
def __init__(self, grad_clip=None):
self.grad_clip = grad_clip
... |
b8044ad93dfc3b50ab748554c52fb60172c4b68c214d6dd075969fa160ba5d92 | Python | 4,514 | 123 | import re
import argparse
import gzip
from multiprocessing import Process,Pool
parser = argparse.ArgumentParser(description='Compare eQTLgen to MetaBrain')
parser.add_argument('meataBrain_eQTL_file',
help='File with eQTL data')
parser.add_argument('eQTLgen_eQTL_file',
help='File... |
946ac543116806e9c113baa646be2903bdeae9257f3704443443e328695833a9 | Python | 4,522 | 145 | """Transform a roidb into a trainable roidb by adding a bunch of metadata."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import pickle
import datasets
import numpy as np
from model.utils.config import cfg
from datasets.factory import get_imdb... |
a42f6b89ed540b3b87250cfa9d6e065e716761fc8f77e7e01bd8048f834669be | Python | 4,526 | 107 | """Load the Winding 2023 larval Drosophila connectome.
Returns a sparse signed weight matrix plus per-neuron annotations.
Signs are NOT in Supplementary-Data-S1 — see nt_signs.py for default conventions.
"""
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
import numpy ... |
e52663096852c6d0e813f04d78a190e21b1757ae599974424e3e6eefd55297d6 | Python | 4,527 | 119 | import numpy as np
import RC
class DualRC :
def __init__( self, Name, Parameter ) :
self.seed = Parameter['seed']
self.prosess_id = Parameter['id']
self.name = Name
self.modelType = 'normal'
self.path = Parameter['path'] + self.name + "_"
Parameter['I'] = Parameter['RC1']
self.RC1 = RC.RC( 'RC1' , P... |
739efc65bf241f222609f94d8f9af349f05f9769276c79e3db83c8283c50d185 | Python | 4,528 | 102 | import numpy as np
import scipy
import scipy.stats
import itertools
class PSTH():
"""
Computes PSTH for a given spiketrain and a list of events
Arguments:
- spiketrain: list of spikes [ms] (array-like)
- events: list of events [ms] (array-like)
- binsize: width o... |
9cc5626bc54bc306fe0befc6f76dc8136f7bb1f73495a8930e86941f055f5fdb | Python | 4,529 | 123 | """
Tests physio_obj.py
"""
import numpy as np
from phys2bids import physio_obj as po
from pytest import raises
# Tests is_valid
def test_is_valid():
test_list = [0, 1, 1, 2, 3, 5, 8, 13]
valid_output = po.is_valid(test_list, list, int)
assert valid_output == test_list
test_array = np.array([0, 1, 1... |
5ecf3e04efb5ca58df07d93cc20bdbb7e9f42f881b32c2599def20527f25cd07 | Python | 4,530 | 134 | # 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... |
696a1392626ce0fd6755bc7c2c1c5353e3e8cf12121d8f23012a7637571f7103 | Python | 4,530 | 127 | # Copyright 2021-2022 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... |
f87337858552afe5d2e54b1af88213600be46abacbc0b825e0d1131cd1ad5f2c | Python | 4,532 | 167 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
import ... |
706d28139a50130e59d873193eeb78e754c287bcd06c740a87b906cb422892a4 | Python | 4,533 | 117 | 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... |
c37dbd6db5a732a9f8d4e72be244ef6699d6fb4c25094ecdbf38c0ed84f2955e | Python | 4,533 | 113 | """
File: cmd_line_arguments.py
Created: 2020/10/08
Last Changed: 2020/10/27
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... |
11525363d888179bc66232493dfe886155532824b473c2f85bbdb6773aa6f985 | Python | 4,535 | 129 | import torch
from transformers import AutoTokenizer, AutoModel, AutoConfig
import pandas as pd
import pickle
import sys
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
print(device)
clinical_bert = sys.argv[1]
#change model name here
if clinical_bert=='huang':
tokenizer = AutoTokenizer.f... |
99915bebc22bc05ad026e63ac7d657b44eb52313fc562112933393fa5f751347 | Python | 4,535 | 120 | """MobileNet"""
import torch.nn as nn
from models.baselines.base_model.basic import _ConvBNReLU, _DWConvBNReLU
__all__ = ['MobileNet', 'get_mobilenet', 'mobilenet1_0', 'mobilenet0_75', 'mobilenet0_5', 'mobilenet0_25']
class MobileNet(nn.Module):
def __init__(self, num_classes=1000, width_mult=1.0, dilated=False... |
9f2abdc675d0859fac0e29aa4fee8b1be18e60264114b125c5aadc3fce070e23 | Python | 4,535 | 60 | import bpy,bmesh,json
from pathlib import Path
import os
from mathutils import Vector
P=Path(os.environ.get('CARLA_MODEL3_WORKDIR',Path(__file__).resolve().parents[4]/'artifacts/tesla-model3'));D=P/'export';D.mkdir(exist_ok=True);(D/'textures').mkdir(exist_ok=True)
bpy.ops.wm.open_mainfile(filepath=os.environ.get('CARL... |
767cb38b5b529bb57872a030cd12a9aeb674c1f12b1fe3e211073e1a7fe6e899 | Python | 4,536 | 114 | # 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... |
2eeb263c044fb419269f450b51f65393a4cc5fcf0b6d4d6f61ce3177a2a5f828 | Python | 4,537 | 117 | #!/usr/bin/env python3
# LAMMPS Documentation Utilities
#
# Scan for duplicate and unused anchor labels in documentation files
#
# Copyright (C) 2017 Richard Berger
#
# 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 ... |
559193bdbb59d8cafb609aaaf188041226331df9aa9bc7dc34f5a23549068f90 | Python | 4,538 | 131 | """Dual Attention Network"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from models.baselines.segbase import SegBaseModel
__all__ = ['DANet']
class DANet(SegBaseModel):
def __init__(self, classes=2, aux=True, backbone='resnet50', pretrained_base=True):
super(DANet, self).__init__... |
9521bd05966e8d7b49c1c089dfb419831ac4abe3bf0e79ed2e2845d663246c1f | Python | 4,540 | 113 | from Lif_Parameters import *
def plot_raster(spike_monitor, preptime, simtime, filename, s=False, save=False):
raster = figure(figsize=[5 * cm_fig_conv, 6 * cm_fig_conv], dpi=600.0)
plot(spike_monitor.t / ms / 1000, spike_monitor.i, ",b")
xlabel('Time (s)')
xlim(preptime / second, (preptime + simtime)... |
6d1932c56199455495ec277780dc4b731b2f417d2e48152d526a072f2125e6d1 | Python | 4,541 | 117 | # Copyright 2021-2022 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... |
a9352cdec7e2f94ae455debef5b63e7a1d559342b2e804eefbf1c06294e11062 | Python | 4,542 | 118 | # 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... |
f10ec773ad3de97fa776a02ec8c84ad11422de6a49ade749b5d171665d1c9b12 | Python | 4,542 | 121 | # basic imports
import os
import pickle
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
def generate_polygons(DR):
P = []
for e, exp in enumerate(DR):
a = int(e/121)
s = e % 121
x = int(s/11)
... |
fb3ce63b98ec6a0d16b156705303e14f398f46e45cfe806ca54c61f9962416c4 | Python | 4,542 | 134 | import time
import math
import numpy as np
def rectangular_crop3d(f, crop_ratio):
half_x = f.shape[0] // 2
half_y = f.shape[1] // 2
half_z = f.shape[2] // 2
# print('half', half_x, half_y, half_z)
x_crop = int(half_x * crop_ratio)
y_crop = int(half_y * crop_ratio)
z_crop = int(half_z... |
391e0129be079da7cedda732ac9dd7bb22acb68cbc239bdc78dc9ebb366ba4c5 | Python | 4,547 | 126 | from __future__ import division
from torchvision import models
from torchvision import transforms
from PIL import Image
import argparse
import torch
import torchvision
import torch.nn as nn
import numpy as np
# Device configuration
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
def load_image(... |
78ab7b575e683f8fddc8d127e2aaa6c4c73a607ca9ea0c560949f60ffb3db453 | Python | 4,547 | 128 | # 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... |
02b20ae96687189ec1e306e9278c01fd5c8fa7ff2ab86cc1b94842cbd8a96b46 | Python | 4,548 | 115 | import warnings
warnings.filterwarnings("ignore")
import numpy as np
import sys
import os
from Bio.PDB import *
from sklearn.neighbors import KDTree
from IPython.core.debugger import set_trace
# Pablo Gainza 2019 - eval zdock results for comparison with MaSIF.
def test_alignment(target_pdb_fn, source_pdb_fn, aligned... |
1a5b754eb1db08f00ab5909d4da7ec3f5f219bd7133aa18fb23d7d05247c54b6 | Python | 4,549 | 167 | __author__ = 'jieqing jiao'
__email__ = "jieqing.jiao@gmail.com"
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import interp1d
def dt2mft(dt):
mft = np.mean(dt, axis=0)
return mft
def dt2tdur(dt):
tdur = dt[
1,] - dt[
0,]
return tdur
def mft2tdur(mf... |
576526c7f12f0c2e29e3dc42e7262b2baf09d71e75d5ce84cb5d41d46bda45b0 | Python | 4,549 | 115 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import os
from warnings import catch_warnings, filterwarnings
import mne
from mne import pick_types
import numpy as np
from numpy.testing import assert_array_equal, assert_array_almost_equal
from eelbrain import load
from eelbrain.testing import assert_dataobj... |
aa0b544976eacf523234bdb8214fbb472463ad41d07f4664d282a2ef2726802e | Python | 4,549 | 119 | import torch
from torch import nn
# only import open3d if built
open3d_built = False
try:
from open3d.ml.torch.layers import FixedRadiusSearch
open3d_built = True
except:
pass
# Uses open3d by default which, as of October 2024, requires torch 2.0 and cuda11.*
class NeighborSearch(nn.Module):
"""Neig... |
b4fe8c771198617357bc486c6e5215108dfe7a82383f71c63dcd3cd49a9193d8 | Python | 4,551 | 142 | import numpy as np
import pandas as pd
from os import listdir, mkdir
from os.path import isfile, join, exists
from PIL import Image
def directory(path):
"""Creates a directory if doesn't exist
Args:
path (string): location to create
"""
if not exists(path):
mkdir(path)
def check_ext(f... |
c45716f8d6479d98b977e98075377c983f7928cbca33eee6780286c04313e674 | Python | 4,551 | 115 | import warnings
warnings.filterwarnings("ignore")
import numpy as np
import sys
import os
from Bio.PDB import *
from sklearn.neighbors import KDTree
from IPython.core.debugger import set_trace
# Pablo Gainza 2019 - eval zdock results for comparison with MaSIF.
def test_alignment(target_pdb_fn, source_pdb_fn, aligned... |
629493cbd1a9a9c610413977fefe3c3273df0d0a5a92d2c2e22d031bd97f963a | Python | 4,555 | 114 | #!/usr/bin/env python3
"""Visualise and validate the pedestrian navigation mesh (navmesh).
CARLA does not expose the navmesh geometry directly, but every point it returns
from get_random_location_from_navigation() lies ON the walkable mesh. Sampling
many such points and drawing them paints the walkable area, and confi... |
e2627e47fb38f82fdcbef98deefa3d746fa80178d83f9cf05f6891d553dc80b1 | Python | 4,555 | 153 | """
StyleMapGAN
Copyright (c) 2021-present NAVER Corp.
This work is licensed under the Creative Commons Attribution-NonCommercial
4.0 International License. To view a copy of this license, visit
http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
Creative Commons, PO Box 1866, Mountain View, CA 94042, U... |
8eb35b4553ab7a9ee0eeda231a22cd8270d545ba320ab113728e6641ca2744e0 | Python | 4,557 | 178 | from pathlib import Path
from typing import Any
import numpy as np
import pytest
import rmsd # type: ignore[import-untyped]
from conftest import RESOURCES
from ppqm import chembridge, mopac, tasks
from ppqm.utils.shell import which
if not which(mopac.MOPAC_CMD):
pytest.skip("Could not find MOPAC executable", al... |
fc49838846780c4abcd3e44a494ac950664c6a4a82e04052d8630c5db579f575 | Python | 4,557 | 108 | # Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
import carla
import unittest
class TestVehicleControl(unittest.TestCase):
def test_default_va... |
14993c722cf6d25309d808ba0511f3575406840e500cc5bdf98e168109f74932 | Python | 4,560 | 110 | from pathlib import Path
from os import chdir
import unittest
from math import sqrt
from nipype.interfaces.base import CommandLine
from qipype.commands import NewImage, Diff, ZShim
from qipype.fitting import ASL, ASE, ASESim, ASEDBV, ASEDBVSim
vb = True
CommandLine.terminal_output = 'allatonce'
class Perfusion(unitt... |
db57ef18f301ea23d373d9254e00b213797785866657aa5bb3bf7386c290acf0 | Python | 4,560 | 160 | from ..utils import get_wandb_api_key, wandb_login
from ..utils import count_model_params, count_tensor_params
from pathlib import Path
import pytest
# Set warning filter to show each warning only once
import warnings
warnings.filterwarnings("once", category=UserWarning)
# Only import wandb and use if installed
wand... |
7012e4d040ec767e665c8c3137f1849a547b50f061b59fc9a57976c461e33d52 | Python | 4,561 | 133 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
import torch.nn.functional as F
from torch import nn
from maskrcnn_benchmark.layers import ROIAlign
from .utils import cat
class LevelMapper(object):
"""Determine which FPN level each RoI in a set of RoIs should map to based
... |
5fc885b3c8329353a4b5e743b0a61c07945b627440a2efc49604ee43c4bdcc2f | Python | 4,562 | 105 | # 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... |
4793e22cc41cb6800a13657fea037f2e477a8db1b5d70c4091c09462cbf0e62e | Python | 4,564 | 116 | __author__ = 'jieqing jiao'
__contact__ = 'jieqing.jiao@gmail.com'
from pathlib import Path
import nibabel as nib
import numpy as np
from tqdm import trange
from ..kt import dt2tdur
from ..tac import TAC
from .regions import extract_regional_values
def image_to_parametric(pet_image, dt, model_name, model_inputs, km... |
b83281aa0421f47d61e50fc465c24e174cfa7d43bcc77d03211731e2207727e0 | Python | 4,565 | 133 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
import torch.nn.functional as F
from torch import nn
from maskrcnn_benchmark.layers import ROIAlign
from .utils import cat
class LevelMapper(object):
"""Determine which FPN level each RoI in a set of RoIs should map to based
... |
badeeaea67a881443a397260f2e101e05ab158fa92375752e6ba49d9c13a53f3 | Python | 4,566 | 132 | # 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... |
ee16c7599560625af60e8bf53463de02c3c63d666f06515b9932ada0a93daa91 | Python | 4,567 | 116 | """
Flywheel zip download support functions
MIT License
Copyright (c) 2017-2021 Mike Tyszka
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 ... |
ef15a9d3f0b99bcf2a00965e51de48721493b27082f2f9b1a00d4cee75aa9d18 | Python | 4,568 | 104 | import numpy as np
from scipy.signal import butter, filtfilt
from scipy.interpolate import interp1d
import torch
from sklearn.preprocessing import StandardScaler
# Clip, filter, and time normalize all sigs in the dataset from one force platform.
# Sigs object must be of shape (N, C, L):
def clip_filt_norm(sigs, fz_th... |
a2c56f42daa161999b2bdc6821b085c907f7b4ca83ce8121499c6c7bbb37d8b7 | Python | 4,569 | 120 | """Optimizes hyperparameters using Bayesian optimization."""
from copy import deepcopy
import json
from typing import Dict, Union
import os
from hyperopt import fmin, hp, tpe
import numpy as np
from chemprop.args import HyperoptArgs
from chemprop.constants import HYPEROPT_LOGGER_NAME
from chemprop.models import Mole... |
e137657bd7b3f3310c19cabfcea94b80971e3627321a85bb40a26e1cc7782262 | Python | 4,569 | 88 | """Soften the legacy falling-rain sprites for the cinematic rain preset.
Run with UnrealEditor-Cmd <project> -run=pythonscript -script=<this file>
-nullrhi -unattended -nosound. Rewires M_Rain without deleting rooted nodes.
The original particle system, world positions, and depth testing are retained.
"""
import unrea... |
eaa6c4669be1ba25c6e78445c14a443f01a2e6e803bcebb8116e5c7f1395a509 | Python | 4,569 | 136 | import gzip
import argparse
import os
parser = argparse.ArgumentParser(description='Remove genes from expression file that have exact same expression levels (likely duplicates), are only found on scaffolds, or have duplicate names.')
parser.add_argument('-g','--gtf', help='GTF file')
parser.add_argument('-e','--expres... |
9decbfe04da7017dbf43afe4998004e6f23e6e5ee37ff0f60e8b1cb7429c23ca | Python | 4,570 | 129 | # 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... |
98b9acbd2ff20e20e72fea63326ff7e3f99aded80a45f7b7933a1cbf9d2c9b3b | Python | 4,572 | 146 | import logging
import numpy as np
import torch
from sklearn.neighbors import KNeighborsClassifier
from scvi import _CONSTANTS
from scvi.core import unsupervised_clustering_accuracy
from .scvi_data_loader import ScviDataLoader
from scvi.core._log_likelihood import compute_elbo
logger = logging.getLogger(__name__)
... |
928f704add80feba41914182039212299ddd820bd07f1dbc5eedc3723b4c760e | Python | 4,573 | 138 |
import math
import numpy as np
from einops import repeat
import torch
from torch import nn
from .layers import *
class StyleGenerator2D(nn.Module):
def __init__(self, out_res, out_ch, z_dim, ch_mul=1, ch_max=512, skip_conn=True):
super().__init__()
self.skip_conn = skip_conn
# dict key i... |
21e10ef162927533be5f8e08ac670f47b5314227b86d2ac769d0bec23ac07fed | Python | 4,574 | 115 | import logging
from typing import Callable
from tensorboardX import SummaryWriter
import torch
import torch.nn as nn
from torch.optim import Optimizer
from torch.optim.lr_scheduler import _LRScheduler
from tqdm import tqdm
from chemprop.args import TrainArgs
from chemprop.data import MoleculeDataLoader, MoleculeDatas... |
f9d94aa0e0f89ea60287e112d8e03c692dd2c6aa81bd810c87f4a51b97b6bb5c | Python | 4,574 | 118 | import tensorflow as tf
import numpy as np
import time
import os
from Network.SR4DFlowNet import SR4DFlowNet
from Network.PatchGenerator import PatchGenerator
from utils import prediction_utils
from utils.ImageDataset import ImageDataset
def prepare_network(patch_size, res_increase, low_resblock, hi_resblock):
# ... |
2d7c497d5b1855768c3515cc42aab28b585f79876e5c7c91241fc134819f3f4b | Python | 4,576 | 126 | # 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... |
178b69c907f5558f8d092a37e5d0e695537cfac2677ac431eb20b34b2e210ea3 | Python | 4,578 | 167 | """
Implements second-order matrix vector product using R-op (forward-mode
automatic differentiation) in TensorFlow.
1) Hessian
2) Fisher
3) Gauss-Newton
"""
import tensorflow as tf
from tensorflow_forward_ad import logger
from tensorflow_forward_ad.fwgrad import forward_gradients
log = logger.get()
def hessian_ve... |
6c24389f613fb8846f857a437bd83ef11940fe02972d0b0757e4bce00bc937f1 | Python | 4,579 | 153 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""
Miscellaneous utility functions
"""
import torch
from torch import nn
from torch.nn import functional as F
from maskrcnn_benchmark.config import cfg
from maskrcnn_benchmark.layers import Conv2d
from maskrcnn_benchmark.layers.dcn_v2 import DCN
... |
b54d635d2574befe0a7a523b6070f06f0132cedabe713bd65600dffd148d923a | Python | 4,579 | 132 | import numpy as np
from sklearn.metrics import confusion_matrix
from sklearn.utils.validation import check_consistent_length, column_or_1d
from sklearn.utils.multiclass import type_of_target
from sklearn.preprocessing import LabelEncoder
from scipy.sparse import csr_matrix
weights = np.array([
[1,1,2,3],
[1,1,... |
dd7c04d6e072453d2f9f3bc09b88d54bf71b1e77386314d198627ff355042069 | Python | 4,579 | 126 | import os
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import numpy as np
from subprocess import Popen, PIPE
from IPython.core.debugger import *
import sys
from Bio.PDB import *
from sklearn.neighbors import KDTree
def test_alignment(target_pdb_fn, source_pdb_fn, aligned_pdb_fn, inter... |
11317bbde6151cd94010182bb13a9843ae1e3b259d479f79e4465fbbd5479f22 | Python | 4,581 | 140 | import argparse
import os.path as osp
import xml.etree.ElementTree as ET
import mmcv
import numpy as np
from mmdet.core import voc_classes
label_ids = {name: i + 1 for i, name in enumerate(voc_classes())}
def parse_xml(args):
xml_path, img_path = args
tree = ET.parse(xml_path)
root = tree.getroot()
... |
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