sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6778996753ba83fd28a62975857ba826446b1d040fc3c400bbc2190d59be8e1c | Python | 7,759 | 224 | import functools
import torch.nn as nn
from utils.pyt_utils import load_model
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152']
def conv3x3(in_planes, out_planes, stride=1):
"""3x3 convolution with padding"""
return nn.Conv2d(in_planes, out_planes, kernel_size=3,... |
65a2f27b0cd3386c097d4345f93f8d1163a8da66f10cddc859398242f9f02f7f | Python | 7,760 | 237 | """Functions for matching the speaker turns in Kaldi CTMs and segments files."""
import csv
from typing import List
from typing import Optional
from typing import Tuple
import pandas as pd
class KaldiFile:
"""Kaldi file template for loading different Kaldi files."""
def __init__(self, filename: str) -> None... |
f04d5551c957069156e91c7042d1017d8936fc97053ee9adac7593e7ff356e30 | Python | 7,760 | 197 | """
This file contains specific functions for computing losses on the FCOS
file
"""
import torch
from torch.nn import functional as F
from torch import nn
from maskrcnn_benchmark.layers import IOULoss
from maskrcnn_benchmark.layers import SigmoidFocalLoss
from maskrcnn_benchmark.modeling.matcher import Matcher
from m... |
9524514ec5aeba9b34592b7fef58020c7dcd7f9ab52d9ce507fe5da48d8367bb | Python | 7,761 | 253 | # -*- coding: utf-8 -*-
"""
Created on Wed Jul 14 15:56:15 2021
@author: zhang.9325
"""
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from keras.preprocessing.image import ImageDataGenerator
from keras.callbacks import LearningRateScheduler
from keras.optimizers import Adagrad
from keras.ut... |
852c568c8d332bfa76c3049b8f6643045b54c9a9cb23fead1e6a8d064e592ed6 | Python | 7,763 | 177 | __author__ = 'jieqing jiao'
__email__ = "jieqing.jiao@gmail.com"
import numpy as np
from math import cos, sin
from scipy.interpolate import interpn
import numpy.matlib
from numpy.linalg import solve
def rigid_p2matrix(translation, rotation):
'''
:param translation: shape (3,)
:param rotation: shape (3,)
... |
1fc4e8dde5b8e93c2c6e5a1c94d01d45147d6727a50ac07374c2b0e6c3a556ee | Python | 7,764 | 222 | from __future__ import print_function, division
import csv
import functools
import json
from logging import root
import os
import random
import warnings
import numpy as np
import torch
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader import default_collate
from torch.utils.data.sample... |
4d85d5e5566f7a248cd6f4b7ce8f2dae807aa62e90442a464feacd115c01847c | Python | 7,765 | 184 | from scipy.signal import correlate as cc
from scipy.spatial.distance import euclidean
from skimage.metrics import mean_squared_error as mse
from skimage.metrics import structural_similarity as ssim
from medpy.metric.binary import dc, hd95
import numpy as np
import pandas as pd
import os
from ddmr.utils.constants import... |
e75382e61b2d3f951343fa70bfed174e97c17fe0a76a54f3708d05e2f682093c | Python | 7,766 | 167 | """ Data reader for AllenNLP """
from typing import Dict, List
import json
import logging
import torch
from allennlp.data import Field
from overrides import overrides
from allennlp.common import Params
from allennlp.common.file_utils import cached_path
from allennlp.data.dataset_readers.dataset_reader import Dataset... |
76ef39e706ad8469cb63ac0d6ccaaa4dcab59e110dfaa3f3accce9d1d55f82d9 | Python | 7,768 | 225 | """Brain viewer"""
from __future__ import print_function
# Import libraries
import math
import os
import os.path
from pathlib import Path
import nibabel as nib
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import matplotlib.patches as patches
matplotlib.use('Qt5... |
f4911522e16a4bbf45a8a5eaf73c9b16ac83fbc9b2efbdc7a170f37894090050 | Python | 7,769 | 193 | 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.gnn_models.node_classification.testing import ... |
38b785f047dd365d5cc68192fd1c6009c254b620d719245cff919318e62a1d89 | Python | 7,772 | 225 | """Brain viewer"""
from __future__ import print_function
# Import libraries
import math
import os
import os.path
from pathlib import Path
import nibabel as nib
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import matplotlib.patches as patches
matplotlib.use('Qt5... |
c1e3d1af1ce1078a5b230228798ef37f5489a6d3a36b2b435053f6d824be280f | Python | 7,773 | 220 | # redminehelper: Redmine helper extension for Mercurial
#
# Copyright 2010 Alessio Franceschelli (alefranz.net)
# Copyright 2010-2011 Yuya Nishihara <yuya@tcha.org>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
"""helper commands... |
a96f00ebbbb1ed81e75c60742948f372c08fd387aeba2a438a9c6c69869dab04 | Python | 7,779 | 216 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
def sum_tensor(inp, axes, keepdim=False):
axes = np.unique(axes).astype(int)
if keepdim:
for ax in axes:
inp = inp.sum(int(ax), keepdim=True)
else:
for ax in sorted(axes, reverse=True):
... |
70390898c37696a74a124537163b79c76709a9cd25f5294c03587946825646ed | Python | 7,780 | 208 | # 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... |
3da6039b975d35d22308c75dc93fc175b31f40535d5ecc26a1a4b358b9747b1f | Python | 7,781 | 192 | import os
import time
import logging
## Plot
import matplotlib
# matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from matplotlib.backends.backend_pdf import PdfPages
import seaborn as sns
import numpy as np
import pandas as pd
def calculate_vmax_vmin(X, cut... |
6d76f298d27d9cbbbd58ce1393ff46730962548ed518ee813af51880480845e4 | Python | 7,788 | 205 | # 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... |
89bcbeb1ff1956bf942c16468097603d9de26f3e81ff86ffb4c07771cbae6bdc | Python | 7,792 | 209 | """Bearer-token authentication.
* Tokens look like ``cc_<id>_<secret>``; only ``sha256(secret)`` is stored in
``<state>/tokens.json`` together with the public ``id`` and a label.
* Verification is a dictionary lookup on ``id`` plus a constant-time compare of
the digest, so timing does not leak which ids exist.
* T... |
b03635f584268ea17ff9d46981182c6ba5609bbec6bad6de743908bc6e0130d7 | Python | 7,793 | 249 | import argparse
import os
import itertools
import torch
import torch.nn as nn
import random
import numpy as np
import clip
from tqdm import tqdm
from dataset.celebahq import CelebAHQ
from dataset.cub import CUBZeroShotText
from torchvision import transforms
class Trainer:
def __init__(self, args):
self.... |
e00713f874d2bdde218ce70295193b6cb471d0c0388e96add963f31dae498387 | Python | 7,793 | 169 | # Code modified from https://github.com/FabianFuchsML/se3-transformer-public
# @inproceedings{fuchs2020se3transformers,
# title={SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks},
# author={Fabian B. Fuchs and Daniel E. Worrall and Volker Fischer and Max Welling},
# year={2020},
# book... |
e065bcd5ca18790a74d8d279e049d2aaf86becbd1019ad9b960835fd1668fa8c | Python | 7,794 | 223 | import csv
import json
import random
from collections import defaultdict
import numpy as np
from pycocotools.coco import COCO
from sklearn.decomposition import PCA
from sklearn.metrics.pairwise import cosine_similarity
data_type = "val2014"
annotation_path = "data/preprocess/annotations/instances_{}.json".format(data... |
88c14d26c4d25bcbf2850d3bfdcd2508fe2040beb693e47c0f5345524bd23b25 | Python | 7,795 | 190 | import warnings
import torch.nn as nn
from ..utils import constant_init, kaiming_init
from .activation import build_activation_layer
from .conv import build_conv_layer
from .norm import build_norm_layer
from .padding import build_padding_layer
from .registry import PLUGIN_LAYERS
@PLUGIN_LAYERS.register_module()
cla... |
69e3a6d5dfb17f9520b063181b6c265a3fd7c0cb6357b61dbefaa3de24999527 | Python | 7,797 | 210 | # 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... |
c02eb1b0f02ac69b20b64af4ec4186d7d810986751af2f73379da1a4649806cb | Python | 7,798 | 184 | import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
import pytorch_lightning as pl
import numpy as np
from omegaconf import OmegaConf
from cotatron import Cotatron
from modules import VCDecoder, SpeakerEncoder, F0_Encoder
from datasets import TextMelDataset, text_mel_collate
class Sy... |
e0e31c7081629182d8a29a6770ff452c848890c3ad86b065d90c271ce84d0687 | Python | 7,800 | 191 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
from functools import partial
import json
import traceback
import imlib as im
import numpy as np
import pylib
import tensorflow as tf
import tflib as tl
import data
import models
import os
... |
316f967ae227f1281392d1406edf107d0d67771846931d63383201456dc85831 | Python | 7,802 | 184 | # 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... |
235ddd0f57fa93a338ab93679eef6f65815caf7d2afb4aff5c85314f24c1da9c | Python | 7,803 | 247 | """Input stimulus object for GIF-like models.
@author : Emerson Harkin
"""
import warnings
import numpy as np
class ModelStimulus(object):
"""Container for input to GIF and related models."""
def __init__(self, dt):
self.dt = dt
self._currentArray = InputArray([], dt)
self._condu... |
4970fe5534fe15ff6a3e0aab7b477c7327635c1bc91d9b845be80468d1ea6166 | Python | 7,811 | 244 | # -*- coding: utf-8 -*-
#
# maggot_models documentation build configuration file, created by
# sphinx-quickstart.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values ... |
bb92c9ad566fc6598b8ed3f2ac1686e68c00debdf8059918b0bbd5033bf988a4 | Python | 7,811 | 146 | import numpy as np
from nipype import Workflow, Node, MapNode, IdentityInterface
from nipype.interfaces.fsl import FLIRT, Merge, ApplyXFM, ImageMaths
import nipype.interfaces.utility as util
from qipype.fitting import MPMR2s, MTSat
from qipype.commands import B1Minus
from qipype.fsl import ApplyXfm4D
from qipype.utils ... |
b6a703a28ab31cff30df36e535c64c291148638d3c1e7880215564d20ab77424 | Python | 7,812 | 220 | # Header variables and parameters.
import sys
import pymesh
import os
import numpy as np
from IPython.core.debugger import set_trace
import importlib
from scipy.spatial import cKDTree
from default_config.masif_opts import masif_opts
"""
masif_ppi_search_cache_training_data.py: Function to cache all the training data... |
d72695a2e325b08494185fdc132308a366ec20f9aeb62ee678998a5a764c1f83 | Python | 7,816 | 187 | """Targeted kNN attack."""
import os
from tqdm import tqdm
import argparse
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.distributed as dist
from torch.utils.data import DataLoader
from torch.utils.data.distributed import DistributedSampler
from torch.nn.parallel import Distributed... |
327f0fe7b28cb3c1ff82150f4686cba923030494d3dd495a1939318c1e46ec5d | Python | 7,818 | 218 | """
properties
Created by: Martin Sicho
On: 06.06.22, 20:17
"""
import re
import tqdm
import numpy as np
from typing import List
from rdkit import Chem, DataStructs
from rdkit.Chem.QED import qed
from rdkit.Chem.GraphDescriptors import BertzCT
from rdkit.Chem import Descriptors as desc, Crippen, AllChem, Lipinski
f... |
2ac4053f526a2b51ec04d61e868348e74c131b9ca916e0452a3470c01cd7d78b | Python | 7,819 | 232 | # -*- coding: utf-8 -*-
from tensorflow.python.util.deprecation import deprecated
from .core import *
from .. import _logging as logging
import tensorflow as tf
__all__ = [
'LambdaLayer',
'SlimNetsLayer',
'KerasLayer',
'EstimatorLayer',
]
class LambdaLayer(Layer):
"""A layer that takes a user-de... |
33ecfa5b9dc79d64bb57a8a4929c2bace7d9e3e662c080b2384ea18faaf35112 | Python | 7,820 | 270 | #%%
import datetime
import time
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from giskard.utils import get_paired_inds
from graspologic.models import DCSBMEstimator, SBMEstimator
from graspologic.utils import binarize, remove_loops
from scipy.sta... |
e2193823d2563ee59cb377c4b619817dff6052a7a85f6c1fea6f9e76ac9d263a | Python | 7,821 | 200 | # Code is copied and adapted from here
# https://github.com/ahendriksen/msd_pytorch/blob/master/msd_pytorch/image_dataset.py
import numpy as np
from pathlib import Path
import imageio
import random
import logging
import re
import torch
from torch.utils.data import Dataset
def _natural_sort(l):
def key(x):
... |
17e522eaa71f8ce11c8e586559404378497c149491c50e450c56481fa605f9ba | Python | 7,822 | 251 | import community
import markov_clustering as mc
import networkx as nx
import torch
from torch_scatter import scatter_max, scatter_mean
from torch_geometric.nn.pool.pool import pool_edge, pool_batch, pool_pos
from torch_geometric.nn.pool.consecutive import consecutive_cluster
from torch_geometric.data import Batch, Dat... |
8a981afe4535682f8a86dda7baa13121b8c28c5acfbc9bd356f9929fa39b97b8 | Python | 7,822 | 207 | #!/usr/bin/env python3
"""
@ Lina Teichmann
INPUTS:
call from command line with following inputs:
-bids_dir
OUTPUTS:
Calculates and plots noise ceilings based on the 200 repeat images for all sensors and each sensor group
NOTES:
If it doesn't exist, the script makes a figures folde... |
0cfdf6516099b649cc435f453531a9c0696f62cd13fcf53d79fbea40a9e81243 | Python | 7,823 | 192 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
5ea091d4c541eb6d7f5ad6ec719c7b1b87a54c2d8646c3d03a1d442dfeec9d17 | Python | 7,831 | 147 | # 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... |
1037e311de16a0a09e665f49b31582b1709ff23b488d48e7570342c622eb4159 | Python | 7,833 | 195 | import os
from tqdm import tqdm
from rdkit import Chem
from rdkit import Chem
import torch
from torch_geometric.data import Data
import networkx as nx
from scipy.spatial import distance
from scipy.sparse import coo_matrix
import numpy as np
from .atom_features import get_available_features_generators,... |
e2e40c17e61ced56e05859ac48fd96a3d8b9a4c0664d152a513132a25be1136a | Python | 7,836 | 309 | # %% [markdown]
# ##
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from graspy.simulations import sbm
from src.data import load_metagraph
from src.graph import preprocess
from src.hierarchy import signal_flow
from src.io import savefig
from src.traverse import ... |
56fd1db9cf4c564afdfb48d7b5ba1c548b162551a3ae57348f3f340e299825b4 | Python | 7,839 | 175 | """
The Trainer class prepares and launches training of a model.
Most importantly, it compiles the tf.keras Model object with according to the
specified optimizer, loss and metrics and implements the .fit method for
training the model given a set of parameters and (non-initialized) callbacks.
"""
import logging
import... |
d489fbe14fc3f7e816e8268feb7a4c611bf5f4d34589db151d20737389dc2599 | Python | 7,840 | 193 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
15fdee87ec4403cc4e1318998ac429d5d1c25e8a8b199baaf8725fcff76011f9 | Python | 7,841 | 228 | import argparse
from datetime import datetime, timedelta
import re
import sys
from bruker2nifti.converter import Bruker2Nifti
import bruker2nifti._utils as utils
from bruker2nifti._metadata import BrukerMetadata
def main():
"""
Parser from terminal with:
$ python2 bruker2nifti -h
$ python2 bruker2nif... |
51ee93d47fea63421a387f0cd568d7cf559a5f1b9c11e70366af44619dbc15a9 | Python | 7,844 | 200 | import logging
from collections import defaultdict
from dataclasses import dataclass
from io import TextIOWrapper
from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Tuple, Type
from sssom_schema import Mapping
from oaklib.datamodels.obograph import Node
from oaklib.datamodels.search import Se... |
d10ed62f412a572d73f35a36c44523f14528ec1ded290ebaa73aea783799354e | Python | 7,844 | 194 | ####################################################################################################
# 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 ... |
15f301726bfdba7e2f2235de538e6316adaa9861a78c5cd04ad4e6217f76d94d | Python | 7,845 | 247 | ##################################
# #
# Last modified 2017/11/08 #
# #
# Georgi Marinov #
# #
##################################
import sys
import os
# try:
# import psyco
# psyco.full()
# except:
#... |
3086dbbdf094ee99b4edccf9695e86aebce1d8ddbe53dec4eb57508321aa0717 | Python | 7,845 | 252 | from __future__ import absolute_import, division, print_function, unicode_literals
import copy
import json
import logging
from collections import OrderedDict
from . import (
fbnet_builder as mbuilder,
fbnet_modeldef as modeldef,
)
import torch.nn as nn
from maskrcnn_benchmark.modeling import registry
from mas... |
fcdbb9ba17e2b4b6ef4d840df9c33771049c0df5831bcde94cf344018e2c3e3f | Python | 7,845 | 194 | from itertools import combinations
import numpy as np
import torch
def pdist(vectors):
distance_matrix = -2 * vectors.mm(torch.t(vectors)) + vectors.pow(2).sum(dim=1).view(1, -1) + vectors.pow(2).sum(
dim=1).view(-1, 1)
return distance_matrix
class PairSelector:
"""
Implementation should re... |
1532c2e93cb132d670214c23a2a922c45f855eb4a002726cef761e4101d58f2f | Python | 7,849 | 215 | """
Copyright (C) 2019 NVIDIA Corporation. All rights reserved.
Licensed under the CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode).
"""
import torch
import torch.nn as nn
class InstanceNorm(nn.Module):
def __init__(self, epsilon=1e-8):
"""
@notice: avoid... |
00359f024235b70be31ea8cb13454eb8be0670bb0efdda482b3907473759f1aa | Python | 7,850 | 208 | import torch
import torch.nn as nn
import torchvision.models as models
import torch.nn.functional as F
from torchvision import transforms
from torch.nn.utils.rnn import pack_padded_sequence
from torch.nn.utils.rnn import pad_packed_sequence
import operator
from queue import PriorityQueue
import itertools
counter = i... |
1b5628818005be2fc9db6f15f143962b4c8687bc150f2a36fb9e05cce18a6d68 | Python | 7,850 | 203 | #!/usr/bin/env python3
"""
@ Lina Teichmann
INPUTS:
call from command line with following inputs:
-bids_dir
OUTPUTS:
Using the MEG data to predict univariate fMRI activation in two ROIs
NOTES:
The plot was made in matlab so it looks the same as the decoding plots (see Step3bb)
... |
439b2930376e9d641b8df3f218acb72706f7975b959ed67857e04da339629e71 | Python | 7,851 | 197 | import numpy as np
import torch
import torch_geometric.transforms as T
import torch.nn.functional as F
from torch.autograd import Variable
from torch_geometric.nn import GCNConv, GAE, VGAE
from torch_geometric.nn import GATConv, GATv2Conv
from torch_geometric.nn import ResGatedGraphConv, TransformerConv
class GCN_poo... |
b2e350cd87d66294986084a0f797bb89876a8219955bbfb66731e3ab405ff482 | Python | 7,852 | 220 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module containing useful metric functions.
Created on Mon Nov 12 09:37:00 2018
@author: nicolas
"""
import numpy as np
from skimage import measure
#%% Metrics for ROI binary detection
def loss_mae(predictions, targets, reduction='mean'):
"""
Compute the (M... |
5df542a9377b0211d52da4565fb2ec5ee1eb5f75736cfd9e8253737c4784b003 | Python | 7,853 | 225 | #%%
import datetime
import os
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from graspologic.match import graph_match
from src.data import join_node_meta, load_maggot_graph
from src.io import savefig
from src.visualization import adjplot, set_theme
from tqdm i... |
17ce115e1877ea5a6c0d36a32c247afdadf1082dca4e10021cca98ca6a32a30d | Python | 7,854 | 203 | # 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... |
0b336b609448a3f8489d715ad335d092ce50ff333a485e77dd2a74adb7ca1fdc | Python | 7,855 | 231 | #!/usr/bin/env python3
"""
File: compare_inter_matrices.py
Created: 2020/04/06
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 Softwar... |
35d4af320c4baf64ba73733c25388b59f04412691a9dcff32077a5a7a2997295 | Python | 7,855 | 251 | import logging
import os
from pathlib import Path
from typing import Union, List
import torch
from torch.utils.data import DataLoader
from .pt_dataset import PTDataset
from .web_utils import download_from_zenodo_record
from neuralop.utils import get_project_root
logger = logging.Logger(logging.root.level)
class D... |
cfa5c614ec328dd1d37dfa1e7f3cd623e7f18e7f20b7fade2af6658e05a84bb3 | Python | 7,856 | 224 | from pathlib import Path
from typing import Literal, List
import yaml
import torch
from the_well.data import WellDataset
from the_well.utils.download import well_download
from ..transforms.normalizers import UnitGaussianNormalizer
from ..transforms.the_well_data_processors import TheWellDataProcessor
class TheWel... |
4ca634253e527c476ae5b4b2bf4316843d7d22482bdb0c7cf3fe7b48980d06b5 | Python | 7,857 | 159 | from drugex.training.scorers.predictors import Predictor
from rdkit import Chem
from sklearn.preprocessing import MinMaxScaler as Scaler
from sklearn.model_selection import StratifiedKFold, KFold
from drugex.logs import logger
class QSARDataset:
"""
This class is used to prepare the dataset for QSAR model ... |
124483917e06b9940c9913794d2930fd77141af4d83ae1949c922cce3c4a6c54 | Python | 7,859 | 149 | # 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... |
7045746bbae06ae36ac6939c966a228a3318802263ff68d267b3f513724431b6 | Python | 7,860 | 195 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
23ccb216ab5b0c0993da789b012cac3b76845284f98f91417e2cfc2696517def | Python | 7,862 | 225 | import os
import random
import multiprocessing
import pickle
import collections
import numpy as np
import torch
from openeye import oechem
from openeye import oegrid
from openeye import oezap
from openeye import oespicoli
try:
from base import VISCOSITY_KEY, ENTITY_KEY
except Exception as e:
from .base impor... |
9c0830ca856a1a2dbe4ea5ef8f0b8110746317f9bfcad47ae5724b0af1ff664b | Python | 7,865 | 210 | import numpy as np
from scipy.optimize import minimize
from functools import partial
from scipy.special import erf, erfcx, erfinv
def erf_times_gauss(X):
return erfcx(X / np.sqrt(2)) * np.sqrt(np.pi / 2)
def log_erf_times_gauss(X):
m = np.zeros(X.shape)
tmp = X < 6
m[tmp] = (0.5 * X[tmp]**2 + np.log... |
e3e2ab0bcce1c4ea6c311114fbb6c369ea0537f187077d72e24c33bdf45302d3 | Python | 7,865 | 186 | """
HMM: Training
=============
This tutorial covers how to train an HMM. We will use MEG data in this tutorial, however, this can easily be substituted with fMRI data.
"""
#%%
# Getting the Data
# ^^^^^^^^^^^^^^^^
# We will use resting-state MEG data that has already been source reconstructed and prepared. This data... |
4affb4466747aa0ae7c078643de3f54fbcc471f5c2ccbd18fb3fddfa9fb98e03 | Python | 7,870 | 182 | # 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... |
a331baa9031d798415659dc4791edcb89a6376f67668aaed74aa8e374d629646 | Python | 7,871 | 222 | import torch
import numpy as np
import networkx as nx
import torch_geometric.utils as pyg_utils
def to_networkx_conv(data, node_attrs=None, edge_attrs=None, to_undirected=False,
remove_self_loops=False, get_map = False):
r"""Converts a :class:`torch_geometric.data.Data` instance to a
:obj:`net... |
2fbb04afda356e31137f749cdcd31df0ce35b5d414776d44be6fc0e0afcc9829 | Python | 7,873 | 191 | import roboscientist.equation.operators as rs_operators
from collections import deque
import numpy as np
import sympy as sp
class ConstantsCountError(Exception):
pass
class InvalidEquationError(Exception):
pass
class Equation:
def __init__(self, prefix_list):
self._prefix_list = prefix_list
... |
3693f14ece0a02e2f68d2ef452099d72b6bd8750956df7910b591d9de89a7bca | Python | 7,874 | 199 | # 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... |
bbf73e3c4cfd4eb16fccd7c20d7137c951cb28a7e269628912cd923e16c4620b | Python | 7,875 | 194 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
c97a9b7ab837f85f9adac3d5b30d7a1392bccbf053522bf868e8483933e866b9 | Python | 7,875 | 218 | import os
import re
import torch
import random
import librosa
import numpy as np
from pysptk import sptk
from torch.utils.data import Dataset
from collections import Counter
from .text import Language
from .text.cmudict import CMUDict
from modules.mel import mel_spectrogram
class TextMelDataset(Dataset):
def __i... |
1e1786df5ba754106766bc6a78fd3528de10fc7d5bf1d14211d1b354d39ffc3f | Python | 7,879 | 248 | import os
import shutil
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from constants.constants import *
from constants.enumerates import DataTypes
def create_tree_dir(tree_levels: dict = None, clean: bool = False, plots: bool = False,
output_dir: str = DIR_OUTPUT_NAME):
... |
5c615956e5cab47bbf66c03232b6ec5895ad427556ffff2ee3f3d6f1e7c37796 | Python | 7,879 | 185 | __author__ = 'jieqing jiao'
__email__ = "jieqing.jiao@gmail.com"
from math import cos, sin
import numpy as np
import numpy.matlib
from numpy.linalg import solve
from scipy.interpolate import interpn
def rigid_p2matrix(translation, rotation):
'''
:param translation: shape (3,)
:param rotation: shape (3,)... |
7078a0e2f82db9896392117b85aef811048e903eda2133b742531bcdd880de37 | Python | 7,879 | 211 | # Built-in
import os
import shutil
from typing import Any
# Third-party
import brian2 as b2
import numpy as np
from brian2.units import ms, second
from scipy import io
# Local
from cxsystem2.core.tools import load_from_file, write_to_file
__author__ = "Andalibi, V., Hokkanen H., Vanni, S."
"""
The preliminary versi... |
c2f5e831e901d06d9796c453afb108ae800a719b688dcccc0ebe1f743edbbf94 | Python | 7,880 | 159 | import random as rng
from pathlib import Path
import cv2
import numpy as np
from .saveFilesC import saveFilesC
class positiveRandomC:
def __init__(self):
super().__init__()
def positiveRandom(self):
acceptance_boolean, overlapping_percentage = (
self.check_if_lesions_and_gland_m... |
8bb4682d2430884e1462239463d2dd49eeb0f48951cf2664e80f26298bb2d899 | Python | 7,882 | 194 | import os
from os.path import join
import collections
import numpy as np
import pandas as pd
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.impute import SimpleImputer, MissingIndicator
from sklearn.pipeline import make_union, Pipeline
from sklearn.ensemble import RandomF... |
8cce607e1c5a3420022864411e285a095f1b040b12504975b4510ad41fbebb10 | Python | 7,882 | 242 | # -*- coding: utf-8 -*-
#
# SIMA documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 28 03:36:31 2014.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All co... |
746630fe8286da753f2bf52530d99d7b19d2aab84e226987e69e7cb4b05fb66b | Python | 7,883 | 171 | # 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... |
bb831c28310edb0d1b8d82cf15b085b62d72818c125975cc25fdf244af2549de | Python | 7,884 | 267 | # 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... |
3218d116c4dec58820ee2e23351d6a2d4f6f1b1cfcd1720af5dd84d670ee5961 | Python | 7,886 | 203 | """
File: inter_zscores_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, eith... |
8fc01bfbf2322532975bc32b062576879d5519d18516a810b9de44a45db08392 | Python | 7,887 | 186 | """Targeted point perturbation attack."""
import os
from tqdm import tqdm
import argparse
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.distributed as dist
from torch.utils.data import DataLoader
from torch.utils.data.distributed import DistributedSampler
from torch.nn.parallel imp... |
9bc44391c169cdb61429ac381f35f2e41d390a5229f824d26f0e2cb68c2bcd92 | Python | 7,889 | 264 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
##################### IMPORTS #######################
import os
import sys
from keras.models import model_from_json
from matplotlib import pyplot as plt
import numpy as np
from keras.callbacks import ModelCheckpoint
from rdkit.Chem.Draw import IPythonConsole
import os,... |
e146aa39e059f65e6d002559d8d37d777d4a1485f1fb145e4ad417270cffd0e5 | Python | 7,890 | 199 | #!/usr/bin/env python3
"""Persistent Alpamayo 2 Super inference service for alpamayo_control.py."""
from __future__ import annotations
import argparse
import json
import os
import socket
import time
import traceback
from typing import Any
import numpy as np
from alpamayo_protocol import WireMessage, recv_message, s... |
2825ccb6f1bc456ca82c2dd0def6ce1b02b76a54fa7e73865b7aa404eb91ca4d | Python | 7,892 | 203 | # 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... |
580871f1595b2501551abfe4ce2f79f851335ed84b969edb1593e216eb3aa201 | Python | 7,892 | 271 | """
The Python implementation of the fast-oopsi algorithm
port from the matlab code by jovo:
https://github.com/jovo/oopsi
@author: liubenyuan <liubenyuan AT gmail DOT com>
@date: 2014-04-16
"""
import numpy as np
import numpy.linalg as lp
from scipy.signal import lfilter, detrend
from scipy.sparse import spdiags, eye
... |
ce10d6064bce1539a6bfe4b925886a929263b0a36e57a08c9a669e6692806a63 | Python | 7,894 | 251 | """Deep Q learning (DQN) for optimizing Nanobeam photonic crystals (using OpenAI Gym)
#Renjie Li, December 2021, NOEL CUHKSZ.
"""
import sys
import gym
import math
import random
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from collections import namedtuple, deque
from itertools impor... |
f4b727ed710c56ede49806c0ccf7e3aa2dae071df5f8a9c3f4a5f8460ff80ea3 | Python | 7,894 | 187 | """Discover mushroom-body compartments from connectome wiring alone.
The larval MB has ~10 anatomically-defined compartments (Eichler et al. 2017,
Saumweber et al. 2018) — each a triplet of (DAN, MBON, shared KC pool) that
performs semi-independent associative learning.
If the wiring is biologically meaningful, we sh... |
0e13b79c8578940a378c36f0b95ba82cb0e23afa67253ed02e9870ced8d961aa | Python | 7,901 | 221 | """
Comprehensive tests for starting_conformations module
"""
import time
import numpy as np
import pytest
from polychrom import starting_conformations
class TestGrowCubic:
"""Tests for grow_cubic function"""
def test_grow_cubic_correct_length(self):
"""Test that grow_cubic produces conformations ... |
250e28bc16f120f27f040b12c5352fe9b3121e0735d542045709eaf8f3675150 | Python | 7,908 | 223 | ####################################################################################################
# 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 ... |
267c8c3ccd5b5ba7cfbbcf9e7428bb5c0481dba084c93c52272d04a0b9bac6c3 | Python | 7,915 | 184 | # 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 now been used to capture 12 records on the FastAI leaderboard.
... |
b54bab669d22307eaed914d01036360a2d19d240134bed85f0f081efc7f4f1bf | Python | 7,920 | 178 | """Public API and CLI regressions for #813 / #757.
Native failures run in bounded subprocesses using the parent's installation.
"""
from pathlib import Path
import subprocess
import sys
import pytest
from conftest import macs3_env, no_core_dumps
from test_callvar_cmd import (REF1, GENOME, REFS, DEL,
... |
e7ca331b7006df6b6d8897c5dfde08ff64cacf7c631c5afbc30c34da5bd5df7b | Python | 7,923 | 152 | # 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... |
7d03cf48dc300931ed4973a83bf29b390cf541f3aeb0f3b98552aa24b54063b1 | Python | 7,924 | 162 | # coding=utf-8
# Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
#
# 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/lice... |
4b65181ab179b9ce8054710be71272fb74b507385d68273c6a3dba9be359bfa6 | Python | 7,927 | 255 | '''
Connectivity
@YX 1210 Edit
'''
import numpy as np
import matplotlib.pylab as plt
import matplotlib
from numpy import linalg as la
from scipy import linalg as scpla
import scipy
# import seaborn as sb
from cmath import *
from scipy.optimize import fsolve,leastsq,minimize
import scipy.integrate
from math import tanh,... |
923afc4d238b0b5729ca6b869438e656c8429aa48289dd7adea04d691ff00f02 | Python | 7,928 | 137 | #!/usr/bin/env python3
"""Unit test of exposure_calib.py without a server: synthetic CARLA-layer / neural pairs with a known EV offset.
A textured road plane (tag Roads, 4..80 m) is rendered on both sides through the sRGB 8-bit encode; the neural side
gets cast shadows (-2 EV patches) and real markings (+1.6 EV patche... |
82336ba4348b16ce67685f08df83071e5640af9a8fc85018428a592b5ef0dffe | Python | 7,930 | 180 | #!/usr/bin/env python3
"""
File: create_psychencode_idlinks2.py
Created: 2021/10/08
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 So... |
638a43bb3448a871eaa58346e484e2e1b59fece6472901997d3b7c38684716a3 | Python | 7,931 | 196 | #!/usr/bin/env python3
"""Read an actor's live telemetry: transform, velocity, acceleration, control.
Select the actor (resolve ambiguity with the world-data skill first):
--id N | --role hero | --filter '*prius*' | --color 255,0,0
| --nearest --near-id N | --nearest --near X,Y,Z
Commands:
show ... |
44485c98ae47abc5a2c7544d01ab72c80fe33410396b1b269ef0a878c7664d1c | Python | 7,932 | 196 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module containing useful functions/classes for model manipulation with PyTorch.
Created on Mon Oct 22 13:54:19 2018
@author: nicolas
"""
import os, sys, shutil
import torch
def weights_initialization(model):
"""Initialize the weights of the given PyTorch model... |
cd13d4f3a9980a19052352936b1f929e1c29032f5701f9078ec7c89a48697a7d | Python | 7,933 | 267 | # Copyright (c) Open-MMLab. All rights reserved.
import functools
import itertools
import subprocess
import warnings
from collections import abc
from importlib import import_module
from inspect import getfullargspec
def is_str(x):
"""Whether the input is an string instance.
Note: This method is deprecated si... |
d0d8fe00584685d27c370de31344fdcb96204254aa79bab36672084dc3568cf5 | Python | 7,933 | 211 | # 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 a... |
c2fea9184f036516bfdde47d986297d1af21363d7e2f8cfd4b10809e92478843 | Python | 7,937 | 200 | from typing import List, Optional
import numpy as np
import pandas as pd
from pydantic import BaseModel
from oaklib import BasicOntologyInterface, get_adapter
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.interfaces import OboGraphInterface
from oaklib.interfaces.semsim_interface import SemanticS... |
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