sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8d66e5aa4b550cbbd45417818f7c224f387ce22ec40f5319c99701eb8c8ca2c7 | Python | 8,814 | 214 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
class ConvBlock(nn.Module):
def __init__(self, in_planes, out_planes, stride=1):
super(ConvBlock, self).__init__()
self.conv = nn.Conv2d(in_planes, out_planes, 3, stride=stride, padding=1, bias=False)
self.bn = n... |
5ece0ac8719faa2b1ea383ec3a05bb7cb23e48ca932f124518cd83f924cee552 | Python | 8,815 | 272 | """
Refer to https://github.com/rosinality/stylegan2-pytorch/blob/master/lpips/networks_basic.py
Refer to https://github.com/richzhang/PerceptualSimilarity/blob/master/lpips/lpips.py
"""
from __future__ import absolute_import
import sys
import torch
import torch.nn as nn
import torch.nn.init as init
from torch.... |
22bf951fedb8e5993b2252b8c6137015c46404521d949fcb27c101740b7fe4cc | Python | 8,816 | 232 | # 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... |
1e875efc651c9fa6df9ab08b6307685441ca140ac23dfa903dfb1c1c8ee69bc7 | Python | 8,819 | 210 | import tqdm
import ipdb
import argparse, sys; sys.path.append('../..')
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.utils.performance.load_exp import exp_exists
f... |
b5511cd93e0b3b94f5d64fc62438f231dbd23cd9b7d1574383422e4fc7b06e04 | Python | 8,819 | 212 | # 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... |
cf75314370de85298d60f249f05dec18ac3f4eec5a40b79033f0930a72d73b56 | Python | 8,821 | 208 | # 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... |
8a8a0bf24c20683768d57d9be664c4bb52b18dfb62d1088f7ac6f2a32424e294 | Python | 8,822 | 319 | """
Copyright (c) 2003 Robert L. Campbell
Copyright (c) 2010 Thomas Holder
Copyright (c) 2013 Suguru Asai
Original by RLC, with extensive modifications and improvements by TH.
Atom B-factor data generated by ptraj (amber) is supported by SA.
Please read below for instructions
contains the functions
data2b_atom(m... |
88ce28365d5dcdf6534ca635a9817710e2f2299958ae995e1d8422f77f3be9f2 | Python | 8,823 | 224 | # 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... |
663d77e83b3058df585e24964f095a9dd8365c55fa16375df330fa366493cc64 | Python | 8,829 | 224 | from collections import defaultdict
from enum import Enum
from typing import Any, Dict, List, Optional, Union
from pydantic import BaseModel
from oaklib.datamodels.obograph import (
ExistentialRestrictionExpression,
LogicalDefinitionAxiom,
)
from oaklib.datamodels.vocabulary import IS_A
from oaklib.interfaces... |
707265bb1e12bb8c9d29d1ddcd08fc68ead6e794d11d33fd108e3ab686bc7217 | Python | 8,831 | 277 | #//=============================================================
#//Copyright (c) 2011 G. Gogoshin
#//Distributed under MIT-style license.
#//(see LICENSE.txt or visit http://opensource.org/licenses/MIT)
#//=============================================================
# This file defines dependence/independence model... |
617308e72b98d500978f164f1c17c768691a3d4352834dd31deaa872c6e0c06b | Python | 8,833 | 262 | """
Plot histograms of the cortical temperatures measured during testing
in each behavior during cooling
The intake data for each behavior should come from the analysis level
of the dataset (i.e. the one taken into R for statistics, and in which
the major preprocessing has already been done)
Version History:
-... |
71f9867dcec8ed1209df9d4e8772bb260b2057f62a95497dadea35779b19bcbe | Python | 8,833 | 222 | #!/usr/bin/env python3
#######################################################################
#######################################################################
## Created on June 29th 2018 to annotate merged peaks
#######################################################################
##########################... |
8f4c2bea4fc179fece6774dd85ba74f669467b3f64ada53997ee2ad2eeb10e5b | Python | 8,833 | 214 | """
File: inter_eqtl_zscore_bars.py
Created: 2020/03/16
Last Changed: 2020/06/03
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, ... |
fb28417b50c7dd71d9cb39971a002b10e1e7bfc4e87d98b24a78e4c20b40adc4 | Python | 8,835 | 236 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 6 23:35:24 2021
@author: Fuyuki Asano
"""
import glob
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import sys
import os
from scipy import signal
import csv
import math
import statistics
import scipy
#mac
#p... |
4ffddf3a71529f52a7d7ca422120b106a0b8f8c366c4c9e1839fcc2cf83ddbfb | Python | 8,836 | 219 | """Launch or adopt a carla-cosmos server.
Two flavours:
* :func:`ensure_server` — the production path: find a container started by us
(Docker labels), or ``docker run`` the image with the state directory
mounted, then wait for readiness and read the initial token from
``<state>/initial_token.txt``.
* :class:`Mo... |
e1a3b839b6ce28b02709b38c2293e2963888ada45c17c5d2f95d65ad72db511f | Python | 8,840 | 273 | import argparse
import cv2
import numpy as np
import os
import torch
import torch.nn.parallel
import torch.optim
import torch.utils.data
import torch.utils.data.distributed
import torchvision.transforms as transforms
import torchvision
from model.unsupervised_model import Model as orgModel
from model.kpt_detector ... |
c9b29b4d11bdd1ccf97f9063039ed8fab03b5c5ded7f078feeca002691fb356b | Python | 8,841 | 224 | ####################################################################################################
# Copyright (c) 2019 - 2023, 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 ... |
6535d7db121dc2ef5c2ccee6e4f907cd098184c60888bfc7c3e08857e33b445d | Python | 8,842 | 238 | # 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... |
de1d9f43d64503e12725bbc9ea4d8b49b7a442ec249601d167a1d4f028996c3e | Python | 8,843 | 232 | # A modification version from chainercv repository.
# (See https://github.com/chainer/chainercv/blob/master/chainercv/evaluations/eval_detection_voc.py)
from __future__ import division
import os
from collections import defaultdict
import numpy as np
from maskrcnn_benchmark.structures.bounding_box import BoxList
from m... |
92e2ddbd00b98801b7c91a74ae466533ec8d7953d4aafb417c7b32031d75e591 | Python | 8,845 | 226 | #!/usr/bin/env python3
#
# Copyright (c) 2018 Hyeshik Chang
#
# 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, modi... |
3e6f065804e9ef33b133dca3ffd6b8e0ba5ad81b1c93617ecdee8d6e4cb8dac1 | Python | 8,855 | 250 | # 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... |
ee6a4f1810e7dc4377e59af96f1871b620de5cb8daba733259dcc91a4c70fcc8 | Python | 8,859 | 323 | # %% [markdown]
# ##
import os
import warnings
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns
from joblib import Parallel, delayed
from scipy.stats import poisson
from sklearn.exceptions import Convergence... |
930febde061fb466ee13f468666fe8920d01ba2a19707432a95a187b3e2dd7ef | Python | 8,870 | 238 | # coding = utf-8
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import gzip
import os
import re
import json
import tarfile
import ConfigParser
from six.moves import urllib
from tensorflow.python.platform import gfile
import tensorflow as tf
import numpy a... |
7f29c3d84f45d5efcf27de9fb0685871153e0f47848ae1e4cb952c7a1bbf25dd | Python | 8,873 | 270 | """Visualization functions for phys2bids package."""
import logging
import os
import matplotlib.pyplot as plt
import numpy as np
LGR = logging.getLogger(__name__)
SET_DPI = 100
FIGSIZE = (18, 10)
def plot_trigger(
time,
trigger,
fileprefix,
tr,
thr,
num_timepoints_expected,
filename,
... |
7fc43528e965feea75f5ee2d2b3c0eec9d5a44a46fe66faff81fdb42411a7a7e | Python | 8,878 | 216 |
"""The data layer used during training to train a Fast R-CNN network.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import torch.utils.data as data
from PIL import Image
import torch
from model.utils.config import cfg
from roi_data_layer.minibatch i... |
62c06349fb20e1c7b687e1cf2bfc3050a3a8e389a42151b0149967409b97216e | Python | 8,881 | 237 | import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
class Sampling(layers.Layer):
def __init__(self, name='sampling'):
super(Sampling, self).__init__(name=name)
def call(self, inputs):
z_mean, z_log_var = inputs
epsilon = tf.random.normal(
... |
7d80e100c0596abceff494fd4ab1450433ddb390b54418f9de0e8d7cac4f4853 | Python | 8,881 | 251 | import math
import os
import sys
import numpy as np
import pytest
from pytest import raises
from phys2bids import io
@pytest.fixture(scope="function")
def loaded_acq_file(samefreq_short_txt_file):
chtrig = 2
header_acq, channels_acq = io.read_header_and_channels(samefreq_short_txt_file)
# just a few qu... |
c990348da813e93d67ca0eab74e4eac7411ff50c0724d27e18312fa108546325 | Python | 8,887 | 228 | # 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... |
d338987751cf989367c520797ac06b1ebc8d53e3a89c0a45750f9363ef9036f8 | Python | 8,888 | 222 | #!/usr/bin/env python3
"""
File: correlate_ct_fractions_to_pcs.py
Created: 2021/02/02
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 S... |
3033634b399251a44d4e3f0858237a6973e045173b52ac37f07bfef05e75b29c | Python | 8,890 | 243 | import gradio as gr
from .compute import run_model
from .logger import setup_logger, read_logs
from .utils import load_ct_to_numpy
# setup logging
LOGGER = setup_logger()
class WebUI:
def __init__(
self,
model_name: str = None,
cwd: str = "/home/user/app/",
share: int = 1,
)... |
3d55aa30dc40207724ddc0b5a220f9b6f1a95a7ccc16731cc00a78763755686d | Python | 8,891 | 318 | from math import prod
import pytest
import torch
import torch.nn.functional as F
from tensorly import tenalg
from neuralop.models import FNO
tenalg.set_backend("einsum")
@pytest.mark.parametrize("n_dim", [1, 2, 3, 4])
@pytest.mark.parametrize("fno_block_precision", ["full"])
@pytest.mark.parametrize("stabilizer", ... |
6418658b69b06011eb3e69b4d05f932853759b53071ee510336ef720d62a735e | Python | 8,894 | 247 | # 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 json
import numpy as np
from logging import getLogger
from .model import update_predictions, flip_attributes
from .util... |
0098eb243a711ba09fa0c3ec37ba7ec170cf8cae2d3c35f0f8aa16e1b7903848 | Python | 8,895 | 266 | import torch
import torch.nn as nn
import torch.nn.functional as F
class TranslationModel(nn.Module):
def __init__(self, vocab, config):
super().__init__()
self.vocabulary = vocab
if hasattr(config, "use_tanh"):
self.use_tanh = config.use_tanh
else:
self.us... |
b7592f08607bda706f9518985ca15de47b2ee8be7de3bc8ff14a377c1fcf4b79 | Python | 8,895 | 239 | import time
import itertools
import scipy
import scipy.stats
import numpy as np
import math
from PIL import Image as PIL_Image
from keras.preprocessing import image
from keras.models import load_model
from recurrent_rsa.rsa_utils.image_and_text_utils import index_to_char, char_to_index
from recurrent_rsa.rsa_utils.conf... |
ec02d7755846c611a9ecf65bfce959ba2976fd71ce76e30720dbf3313c0c85f5 | Python | 8,895 | 224 | import random, sys
from typing import Union, List
import os
from networkx.classes.function import to_undirected
import networkx as nx
import ipdb
import torch
import numpy as np
import matplotlib.pyplot as plt
import torch.nn.functional as F
from numpy import ndarray
from torch_geometric.utils import to_networkx
from t... |
36b136b7eef0e2a930d009080ddef6e9eaa7b823d1a5c0d89638a78bc27ef31f | Python | 8,903 | 253 | import logging
import numpy as np
import torch
from torch.nn import functional as F
from scvi import _CONSTANTS
from scvi._compat import Literal
from scvi.core.data_loaders import AnnotationDataLoader
from scvi.data._anndata import get_from_registry
from .inference import UnsupervisedTrainer
from .trainer import Tra... |
c05ae96958f54010caa8fc76f830614d8dcab1fd86c0f279f57f54a5c3e36eaa | Python | 8,903 | 247 | # 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... |
afd5095260d259e941a120a06214f7c6dc16c3c5b33bfa6febe2c540e51810c4 | Python | 8,908 | 266 | # Copyright 2023 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... |
b258c9ea90ec2749cecff8b0ca1cbf8d07dd7dc916adc288f7dcaa290344e7d7 | Python | 8,910 | 160 | 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
import h5py
from tqdm import tqdm
from functools import partial
import numpy as np
from scipy.spatial.distance import euclidean... |
e1ba787d817933131db14a6fa87cb3198248103e52446cb183da39ffa087c41d | Python | 8,910 | 273 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import os
import numpy as np
from numpy.testing import assert_array_equal
import pytest
from eelbrain import Dataset, Factor, Var
from eelbrain._exceptions import DefinitionError
from eelbrain.pipeline import *
from eelbrain.testing import assert_dataobj_equal,... |
e788da1edc9185edc4b29dcbe7dd6fb803bf72954174868451e01e0ab8ca82e0 | Python | 8,911 | 182 | #! /usr/bin/env python3
"""7-camera world-scenario demo: capture with the NVIDIA AV rig, export the ClipGT scene
package, submit it to Transfer 2.5 auto/multiview (``hdmap_bbox``) and, optionally, the
front camera to Cosmos 3 as a ``wsm`` control.
python av7_world_scenario.py --port 2000 --seconds 3 --out ./clips ... |
48e08bcefb5871953689bbeb6142c1bdf5a418ec209d6a754c025c10f32959a3 | Python | 8,914 | 211 | import mne
import numpy as np
import matplotlib.pyplot as plt
import os
from mne.preprocessing import ICA
from autoreject import get_rejection_threshold
from autoreject import (AutoReject, set_matplotlib_defaults)
## logging info ###
import logging
from datetime import datetime
logname = './logs/' + d... |
5a20414cfca161e9bbb68ab01f07a5fd73b020ee2d881687e6e70500461b3f44 | Python | 8,916 | 269 | import argparse
import torchvision.datasets as datasets
import torchvision.transforms as transforms
import torch.optim as optim
import pickle
import datetime
from netClasses import *
from netFunctions import *
from plotFunctions import *
parser = argparse.ArgumentParser(description='Updates of Equilibriu... |
ad0989d9ea6c3528911cdd7022744824bc849b041836a525a200fb7ced8ab00a | Python | 8,920 | 185 | """Build the reviewed optical-detail revision from the detail master.
Reflector proportions follow the local original-generation headlight photograph.
These surfaces approximate visible construction; they are not optical CAD.
"""
import bpy
import bmesh
import json
import math
import os
import numpy as np
from pathlib... |
94c2aab19a8f6ebc6b8c2f5ca790064dee9e42720ff425435d1ed2f15e86039f | Python | 8,924 | 244 | import torch
import torch.nn as nn
from mol_tree import Vocab, MolTree, MolTreeNode
from nnutils import create_var, GRU
from chemutils import enum_assemble
import copy
MAX_NB = 8
MAX_DECODE_LEN = 100
class Motif_Generation_dfs(nn.Module):
def __init__(self, vocab, hidden_size, device):
super(Motif_Gener... |
29fc6418f26b041d65943c057fbcf5bf32a9cc71d2b3882e550ae41758c06306 | Python | 8,925 | 296 | """
This module provides the `Sequence` class. This class is the abstract
base class for biological sequence collections (e.g. genomes).
"""
from abc import ABCMeta
from abc import abstractmethod
import numpy as np
from ._sequence import _fast_sequence_to_encoding
def sequence_to_encoding(sequence, base_to_index, ... |
addd72837ed25549c88a8e559247b07bd44ef7f3d14a95577fa5f5260d692111 | Python | 8,925 | 303 | """
Training an FNO on Darcy-Flow
=============================
We train a Fourier Neural Operator (FNO) on our small :ref:`Darcy-Flow example <sphx_glr_auto_examples_data_plot_darcy_flow.py>`.
This tutorial demonstrates the complete workflow of training a neural operator:
1. Loading and preprocessing the Darcy-Flow ... |
942cafb524386dec805d3b92eba474f07ae423626da0b8c09ed495044d156eec | Python | 8,927 | 240 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from layers import *
from data import voc, coco, tt100k, tt100k45
import os
class SSD(nn.Module):
"""Single Shot Multibox Architecture
The network is composed of a base VGG network followed by the
added ... |
75b4467729593791e3292df9d991ccfc28276647e40d1152ad2dad4fb6640881 | Python | 8,928 | 250 | import torch
import numpy as np
from scipy.special import expit
from scipy.integrate import odeint
class Network(torch.nn.Module):
def __init__(self, items_n, h1_size, w1_weight_std, w2_weight_std, non_linearity=torch.relu_, readouts=1):
"""Two-layer neural network to calculate the pairwise relationships ... |
66a127937548bfddb9da77b5fb120f4c543fd981441a9980f4c9e1f044348dd3 | Python | 8,933 | 194 | # 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... |
76f2bcd0b86af16ae81ef942fa83a0cc9345caf775819e5e916279a4f49ae0b4 | Python | 8,945 | 209 | # 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... |
0e3bc84d95c21ce493b7e43a215452b4f027b48d7dadab2c23f49bf53f5c1009 | Python | 8,946 | 290 | #%% Load
from operator import itemgetter
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from graspy.cluster import KMeansCluster
from graspy.embed import LaplacianSpectralEmbed, OmnibusEmbed
from graspy.models import DCSBMEstimator
from graspy.plot im... |
f520fe73c3cfa495dfe4c1979b6b84f374dd489ac1ed4cb2ed4af8ca70c35f6f | Python | 8,951 | 259 | #!/usr/bin/env python
# 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>.
"""
Configure and inspect an instance of CARLA Simulator.
For further detail... |
df4c9928b3927ea90c2a1fad362559f980708206383887e2bb59a629bcd62ff2 | Python | 8,952 | 213 | import os
import multiprocessing
from joblib import Parallel, delayed
from gpuparallel import GPUParallel
from gpuparallel import delayed as GPUdelayed
import numpy as np
import mne
import torch
from torch.nn import Linear, ReLU, Conv2d, MaxPool3d, Module
import torch.nn.functional as F
from RV.model.utils.smoothi... |
606f1fb90a205f6122f3cfb5b149c9a8ae1f96447437827db1283757d32bd329 | Python | 8,955 | 273 | """
function plot_unpaired_data_for_Magnum
INPUT:
- csv file containing behavioral data with cross-referenced temperature
values for each trial
OUTPUT:
- Figure with two axes showing:
1. Bar plot of overall performance ( correct) for each noise
condition in cooled and control testing, with individual session
... |
6315f06d37d2db75ad0e3984ce2295c0419485e7c5cbe8e57619c67a62abfdb1 | Python | 8,955 | 231 | #!/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
"""
... |
2c7eb7a94202fba7cd6a1f5a1b09cc0f39e2ef60c542e93d3a1243f147f1b5b6 | Python | 8,959 | 158 | 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
import h5py
from tqdm import tqdm
from functools import partial
import numpy as np
from scipy.spatial.distance import euclidean
... |
2f54751d5c6e3bbbfb3efc4835eb038743b5e165cc286fe59accb4bdab8e08cc | Python | 8,960 | 198 | # 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... |
7aefccf85d71d94caaa5649b537a50a060a834b49490fed8f958429d22cf501f | Python | 8,960 | 228 | import torch
from torch_geometric.data import Data, Batch
class BatchMasking(Data):
r"""A plain old python object modeling a batch of graphs as one big
(dicconnected) graph. With :class:`torch_geometric.data.Data` being the
base class, all its methods can also be used here.
In addition, single graphs c... |
84760a3eda562fdb6d5721fa39d888d4f71c7ae959334cb5db9f10fdd78932e1 | Python | 8,969 | 271 | from ase.md.langevin import Langevin
from ase import units
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.io import read, write, Trajectory
import numpy as np
import torch
import sys
import glob
import toml
import argparse
from pathlib import Path
import logging
from PaiNN.data import A... |
a11337b1b028197b7917ab256a7e25c2309ce1a64634ef714dd8bcc6737f4147 | Python | 8,969 | 242 | import argparse
import glob
import os
parser = argparse.ArgumentParser(description='Generate featureCounts files.')
parser.add_argument('cram_base_directory', help='Directory with cramFiles')
parser.add_argument('jobs_directory', help='Directory to write jobs to')
parser.add_argument('output_directory', help='Outputdi... |
e2baef50d5c4cad51517d9283c3bf021910840b10afc19b4f09ae1ec323aa395 | Python | 8,969 | 223 | # Model validation metrics
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import torch
from . import general
def fitness(x):
# Model fitness as a weighted combination of metrics
w = [0.0, 0.0, 0.1, 0.9] # weights for [P, R, mAP@0.5, mAP@0.5:0.95]
return (x[:, :4] * w).sum(... |
df784318c6f7f3b57552bf81630c81670bbe5dee6c7ec492b7cf44d8d2537c25 | Python | 8,970 | 221 | import os
from os.path import join
import numpy as np
import pandas as pd
from collections import OrderedDict
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import ShuffleSplit
from sklearn.model_selectio... |
c307532a15ad3607abf70c6adebd18993bd6c512ce721262505a9ee939e06aae | Python | 8,972 | 176 | """
Copyright Dejan Kostyszyn 2019
This method trains the network.
"""
import ReadData as rd
import numpy as np
from matplotlib import colors
import torch, os, nrrd, time
from model.UNet import UNet
import matplotlib.pyplot as plt
from options.test_options import TestOptions
import utils, csv, sys
from os.path import... |
1cefbf9359722c5c5f12bf0a50762546eeb48d240214ed2ccf1b68d6055337ea | Python | 8,973 | 278 | import torch.nn as nn
import torch.nn.functional as F
from utils.function import FakeQuantize
import math
def calcScaleZeroPoint(min_val, max_val, num_bits=8):
qmin = 0.
qmax = 2. ** num_bits - 1.
scale = float((max_val - min_val) / (qmax - qmin))
zero_point = qmax - max_val / scale
... |
fe35748eeae55dc0a8d6a46b8727c3fb667655ca21187ba0908986e1ddb0d1bf | Python | 8,975 | 252 | """
File: settings.py
Created: 2020/06/29
Last Changed: 2021/11/22
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, either versio... |
8615f12979c2bc1ef9ca7b999b2f065477846825d55b4197884674e1739fa4ad | Python | 8,978 | 221 | # coding=utf-8
# Copyright 2020 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... |
44970b38e67bce15e8f5cafa0270d46c5d145b55e4c3377c81c3761721b1b801 | Python | 8,979 | 175 | # Copyright 2020-21 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... |
67734c5f444b456874d518b405512283dae462d77adf4fc9c11166cf93b27ef9 | Python | 8,982 | 228 | #!/usr/bin/env python3
"""
@ Lina Teichmann
INPUTS:
call from command line with following inputs:
-bids_dir
OUTPUTS:
- plot showing percentage of data we lost after preprocessing
- plot showing the time-resolved euclidean x/y coordinates from the central fixation
- plot showing the ... |
f81b991e3cb3d653670ced5aeb3fa93213108bb8d2e523117e9bdf2671abbde6 | Python | 8,985 | 242 | from math import sqrt
import torch
from tqdm import tqdm
import matplotlib.pyplot as plt
import networkx as nx
from torch_geometric.nn import MessagePassing
from torch_geometric.data import Data
from torch_geometric.utils import k_hop_subgraph, to_networkx
sys.path.append("..")
EPS = 1e-15
class GNNExplainer(torch.... |
a6049d494658b4f7d52a242da934866089edf561565c0bcabb97108a58a7fc29 | Python | 8,988 | 278 | # Based off code from: https://github.com/google-research/reverse-engineering-neural-networks/blob/master/renn/rnn/fixed_points.py
import torch
from torch import nn
import torch.nn.functional as F
import numpy as np
import copy
from scipy.spatial import distance
class fixedPointNetwork(nn.Module):
"""
Cre... |
3b58bcfb3657506e2d4b779978af672141e2c38870a6faca99c532e48f97c562 | Python | 8,990 | 243 | import logging
import time
from dataclasses import dataclass
from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Tuple
import requests_cache
from oaklib.datamodels import obograph
from oaklib.datamodels.association import Association
from oaklib.datamodels.search import SearchConfiguration
fro... |
a8dce281f3a679e7ed908bfea9325be684d011a8dd6d2b7f41a7550764fe7cc4 | Python | 8,993 | 227 | import torch
from torch import nn
import torch.nn.functional as F
from .channel_mlp import LinearChannelMLP
from .segment_csr import segment_csr
class IntegralTransform(nn.Module):
"""Integral Kernel Transform (GNO).
It computes one of the following:
(a) \\int_{A(x)} k(x, y) dy
(b) \\int... |
8a591cd698020231a30f4709ffbfca371a27ef69c0f09de882eae206ee7a48ed | Python | 8,994 | 221 | import os
from os.path import join
import numpy as np
import pandas as pd
from collections import OrderedDict
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import ShuffleSplit
from sklearn.model_selectio... |
adbb6614ad51d0364d19f750f50c14dbb8b51c145dc88ae86d2af4403a09d965 | Python | 8,995 | 233 | import argparse
import os
import numpy as np
import pandas as pd
import vtk
from collections import defaultdict
from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
import pymetis
from glob import glob
# Seed for reproducibility
np.random.seed(42)
def read_vtk_mesh(file_path):
reader = vtk.vtkPolyDataRea... |
f5814111e603add64a3476441a848e137160b705eb76b2604143fe0f0ea4e5eb | Python | 9,000 | 176 | # 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... |
7f27f396450337732b6748aaefbeb335ef0f83b33da7ba197cede25a8e838c6b | Python | 9,001 | 219 | from __future__ import absolute_import
# --------------------------------------------------------
# Faster R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick and Sean Bell
# --------------------------------------------------------
# ---------------... |
fd6cc42a35005720f22b890a4fdeed54bea2dd8396e36edad2eccf1140e9ae1b | Python | 9,006 | 282 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 2 14:32:25 2021
@author: antonio
"""
import warnings
import itertools
def warning_on_one_line(message, category, filename, lineno, file=None, line=None):
return '%s:%s: %s: %s\n' % (filename, lineno, category.__name__, message)
warnings.forma... |
74f94a4a08d5746b11f765610d922f1a1c27303a7cd3886e10f55e7a3a3f2f07 | Python | 9,007 | 209 | # 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... |
ca4fa9819eea9f75b1bec06c0743f947c2d0d5b9160dc1f71c14b451ffafa3dc | Python | 9,012 | 242 | # 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... |
339df828874e65fc35f96e37d430959bb49ef36fec1ce592d56766e0399eab8e | Python | 9,014 | 243 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
class FastSal(nn.Module):
def __init__(self, classes=2, aux=False, pretrained='MobileNetV2_pretrain.pth'):
super(FastSal, self).__init__()
self.context_path = MobileNetV2(pretrained)
if pretrained is not ... |
bd8344cfc19de32679bdedf6238b2fbf595b666d1eb8a1ec993e94e090fae8ef | Python | 9,016 | 342 | import argparse
import gzip
import tabix
import math
def main():
parser = argparse.ArgumentParser(description='LiftOver utils.')
parser.add_argument('--mode', choices=['gwastobed', 'liftovergwas','updatetrityperpos','updatetrityperrsid'], help="Type of program to run", required=True)
parser.add_argument('--in... |
4e3d447fab1524bd17b13646a8f5a7b2b03f156956dc73fa17c99cd525426a80 | Python | 9,023 | 240 | import os
try:
# for Python2
import Tkinter as tk
import tkFileDialog
except ImportError:
# for Python3
import tkinter as tk
from tkinter import filedialog as tkFileDialog
import webbrowser
from bruker2nifti.converter import Bruker2Nifti
from bruker2nifti.__init__ import __version__ as versio... |
22c7800515db33d94e9f08a920255ce2c6e38c126dc495e9fd00c3901b95ed29 | Python | 9,024 | 294 | import numpy as np
import imageio
import PIL.Image as pilimg
import tensorlayer as tl
__all__ = [
'get_img3d_fn',
'rearrange3d_fn',
'get_and_rearrange3d',
'get_img2d_fn',
'get_lf_extra',
'lf_extract_fn',
'write3d',
'normalize_percentile',
'normalize',
'normalize_constant',
... |
29573d94de13008cf104eaa120f949a94f1af7c314f3d93d42e17a39b088957d | Python | 9,025 | 239 | ####################################################################################################
# Copyright (c) 2019 - 2023, 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 ... |
5354b7b354c421799336cf3b8644577d0b87f5e4fff631ea72cc6abc70bd948b | Python | 9,027 | 315 | import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from graspologic.plot import heatmap
from mpl_toolkits.axes_grid1 import make_axes_locatable
from seaborn.utils import relative_luminance
from pathlib import Path
from .theme import set_theme
from .utils import bound_text... |
e9fcb249334a1d7e4d424db85f125d633b4d05f98856f727b830aceca8241b35 | Python | 9,031 | 385 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import scipy
import seaborn as sns
from graspy.match import GraphMatch
from graspy.plot import heatmap
from graspy.simulations import sbm
from src.data import load_metagraph
from src.graph import pre... |
e28de2ed617f1f0e04b276caac149d19dd92fed95d1f4f46976194cf4e68b39d | Python | 9,032 | 211 | '''
Definitions of geometrical objects.
'''
import numpy as np
from mesh.operate import transform
def ellipsoid_create(name, position=(0, 0, 0),
lengths=(1, 1, 1),
axe1=(1, 0, 0),
axe2=(0, 1, 0),
velocity=(0, 0, 0),
... |
f7a7abde133f8c3c92fb067188e6d73e8cdd9169a862cf1a21f387d76a4b2432 | Python | 9,032 | 218 | #!/usr/bin/env python3
# Copyright 2020 Maxim Korenevsky (STC-innovations Ltd)
# Apache 2.0.
import argparse
import os
import numpy as np
from sklearn.cluster import k_means
import kaldi_io
import scipy
from sklearn.cluster import SpectralClustering
'''
Spectral Clustering based on binarization and automatic th... |
36320ade6fce2295c36c9e5d3cb01c7f7a8a6655d46287380d5e94e7dea07842 | Python | 9,034 | 229 | """
Normalization Layers
====================
This tutorial demonstrates normalization layers designed for neural operators.
Normalization is crucial for:
- Stabilizing training dynamics
- Accelerating convergence
- Improving generalization
- Handling different data distributions
The tutorial covers `InstanceNorm`, ... |
979924cdf642bea68e3ee01ec33f725f9f9d2b779f91806b9818d3500b7d078b | Python | 9,035 | 211 | # 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... |
be5be9233058ad728f21bdb69547262b86a5f146aeab657dc4681bf8b172ecc4 | Python | 9,035 | 191 | # This file is part of me-features-to-mol-ID-mapping.
#
#
# Copyright © 2021-2022 Blue Brain Project/EPFL
#
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the APACHE-2 License.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANT... |
da7e1ea3d99e7605719a968217f447ccbc79c6a054458005d57bc9d79f88048d | Python | 9,036 | 261 | import datetime
import numpy as np
import os
import re
import shutil
from utils.SGCN.common import names
def path(parts):
return os.path.join(*parts)
def mkdir(p, overwrite=False):
if os.path.exists(p) and overwrite:
shutil.rmtree(p)
if not os.path.exists(p):
os.makedirs(p)
def parse_... |
d726945f2403ed5127634594958b43f667748bf8515ba9a2665af4b3fb78a7b1 | Python | 9,037 | 264 | import os
import copy
import numpy as np
import pandas as pd
import math
import random
import matplotlib.colors as colors
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
from siVAE.data import data_handler as dh
from siVAE.util import reduce_dimensions
fro... |
568ac22639556523abb2dd42d359afe894063bf2591682dcf18432f169f3fb88 | Python | 9,040 | 264 | import os,gc
import copy
import numpy as np
import pandas as pd
import math
import random
import matplotlib.colors as colors
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
from siVAE.data import data_handler as dh
from siVAE.util import reduce_dimensions
... |
684edd50cba29b09a70ff7617ce2107a3fdba9e0adab19bb246d2748f6247485 | Python | 9,041 | 225 | import numpy as np
from ase.data import atomic_numbers
from scipy import linalg
from sklearn.metrics.pairwise import euclidean_distances, cosine_distances
def div_mat(mat, n):
split_mat = []
div_1, mod_1 = divmod(mat.shape[0], n)
div_2, mod_2 = divmod(mod_1, div_1)
for i in range(mod_2):
split_... |
a0cb6da3fb9795c6333625487a788287afad8fbfa52865d6cba29b8d7141700d | Python | 9,046 | 280 | '''
@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_train_... |
acc114fb04cc08208523e69b4e34e3895f1c33d0d85fc9e33f02fe6ae2d0d596 | Python | 9,048 | 222 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2020 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
f73fc1ad3d76fac3765f454d1774f6fa5558c2609a3ed6225c382148e1480c99 | Python | 9,051 | 208 | # Ranger deep learning optimizer - RAdam + Lookahead + Gradient Centralization, combined into one optimizer.
# https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer
# and/or
# https://github.com/lessw2020/Best-Deep-Learning-Optimizers
# Ranger has been used to capture 12 records on the FastAI leaderboard.
# Th... |
9fd444a9528735d8492eecd8b2c65b6e1ab87dbe4e7c188e51cf11d1faaa582a | Python | 9,056 | 292 | import pandas as pd
from os import mkdir, path
from shutil import move
from pathlib import Path
from datetime import date
import sys
from SVRecords import SVGrouper, SVAnnotator
def make_exon_gene_set(protein_coding_genes):
df = pd.read_csv(protein_coding_genes, sep="\t")
return set(df[df.columns[5]])
def ... |
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