sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ba7f92683e5b316684f4834613d69bed41c0825d63f8c4f6ac842d35d5ba2143 | Python | 3,815 | 92 | # 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... |
426aa7bb65524e58b011703d59d5ff07d4b5b762883a68c950247f20b8b74f55 | Python | 3,816 | 126 | import torch
import pytest
from ..otno import OTNO
# Fixed variables
in_channels = 9
out_channels = 1
hidden_channels = 16
n_modes = [16, 16]
lifting_channel_ratio = 3
projection_channel_ratio = 3
n_layers = 4
# data parameters
n_s_sqrt = 18
n_target_points = 100
@pytest.mark.parametrize("positional_embedding", [N... |
d0e6db83f2523bec2a773507568dde6cd6c254261c4e23763befa4b30615fab1 | Python | 3,816 | 94 | import unittest
from oaklib import get_adapter
from oaklib.datamodels.obograph import (
DisjointClassExpressionsAxiom,
ExistentialRestrictionExpression,
)
from oaklib.datamodels.vocabulary import PART_OF
from oaklib.utilities.axioms.disjointness_axiom_analyzer import (
generate_disjoint_class_expressions_a... |
a0dbf5bc48525d0c10d90a832f9fb065f5dfc3baaa43f08015345726cd2deb61 | Python | 3,818 | 94 | from __future__ import print_function
import numpy as np
import os
import matplotlib.pyplot as plt
import torch
def _get_detections(dataset, retinanet, score_threshold=0.05, max_detections=100, save_path=None):
""" Get the detections from the retinanet using the generator.
The result is a list of lists such... |
dfe25300bb133769a1b4ebebf1cb8a6cdba06f92e11d81042be318bb5464398b | Python | 3,818 | 109 | # 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 --------------------------------------------------------------
# If ex... |
e9ba9000d5a27d2d4d7056276a23753f1f4e12f372d06e8b1895dd3ebebc9796 | Python | 3,819 | 67 | import numpy as np
import copy
import h5py
import sys,os
import pandas as pd
import scipy.sparse
import pickle
sys.path.append('/home/thijs/repos/dnp-code/PGM3_correct/source/') # the path where the folder PGM is.
sys.path.append('/home/thijs/repos/dnp-code/PGM3_correct/utilities/') # the path where the folder PGM is.
... |
bf2658561a187ae6ba74aced58891e52d670ad308a44a20f8f926065cb3c44ac | Python | 3,820 | 105 | # 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... |
4b3503c1f776b4d3afa6965112579f88e1bcf925a37a7b499d1648633b453825 | Python | 3,821 | 83 | import json
from carla_cosmos_server.auth import TokenStore, bootstrap
from conftest import submission, upload
def test_token_store_roundtrip(tmp_path):
store = TokenStore(tmp_path / "tokens.json")
tok = store.create("ci")
assert tok.startswith("cc_")
tid = tok.split("_")[1]
assert store.verify(... |
cea0f6085f16ca2bee039a08c6ddc4c2b15f5c333d9564f637721dd598a99223 | Python | 3,821 | 132 | # -*- coding: utf-8 -*-
#Model config.
#Training config
import json
import pathlib
INPUT_SHAPE = "input shape"
KERNEL_SHAPE = "kernel shape"
POOLING_SHAPE = "pooling"
LEARNING_RATE = "initial learning rate"
SEGMENTATIONS = "segmentations"
OPTIMIZER = "optimizer"
LOSS_FUNCTION = "loss function"
STRIDE = "str... |
6757f063515a47b17bfe0a8c45b482a25e6dbf891da2493374795d1cb55485e6 | Python | 3,822 | 97 | import logging
import unittest
from oaklib.datamodels.search import SearchConfiguration
from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation
from oak... |
9175a693dc0bf1043274f47b169aca469d90452c70eb8c3d1bc623fb1291255a | Python | 3,823 | 101 | import logging
import numpy as np
from .batch_sequence import BatchSequence
from .random_batch_sequence import RandomBatchSequence
from .balanced_random_batch_sequence import BalancedRandomBatchSequence
logger = logging.getLogger(__name__)
def batch_wrapper(generator, x_shape, y_shape,
x_dtype=np.f... |
f4a675babf5d9e6035bc6457e7ec348470d4bda1342e90996af4ecf28178e9ea | Python | 3,823 | 133 | """
http://pymolwiki.org/index.php/spectrumany
(c) 2010 Thomas Holder
License: BSD-2-Clause
"""
from pymol import cmd, stored
expression_sc = cmd.Shortcut(
[
"count",
"resi",
"b",
"q",
"pc",
]
)
def spectrumany(
expression, color_list, selection="(all)", minimu... |
2a338c33ea339f991cf9133be408dd0c007828430e65a16a706a6bf4bb642b3a | Python | 3,826 | 98 | # basic imports
import os
import pickle
import numpy as np
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.misc.gridworld_tools import make_open_field
def single_run(world: dict, number_of_replays: int = 20, batch_size: int = 20, mode: s... |
2184d982779de5b49e615a7363b2264f68528be2d429ef59b72db7d322159a6f | Python | 3,829 | 109 | """
File: create_extra_cov_matrix.py
Created: 2020/10/20
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 Foundation, either ver... |
4c2e46e39bbce1da0b3fc2850a9c2fa436b7776764ef8f8813c8da7cef05bfad | Python | 3,832 | 96 | """
Some analysis of informational content of TLDR-Auth and TLDR-PR
"""
import os
import csv
from collections import Counter, defaultdict
INFILE = 'tldr_analyze_nuggets/tldr_auth_pr_gold_nuggets_2020-03-31.csv'
# Q1: How many nuggets do TLDRs contain?
# A: Interesting, both author and PR have nearly identical di... |
6962129e016ba8b0bbc84b85b1e08f49cde03aee36584744d67bce8a43d35187 | Python | 3,832 | 107 | from typing import List, Union
from pathlib import Path
import torch
from .mesh_datamodule import MeshDataModule
from .web_utils import download_from_zenodo_record
from neuralop.utils import get_project_root
class CarCFDDataset(MeshDataModule):
"""Processed version of the Car-CFD dataset.
CarCFDDataset... |
cb49f0aadb4577b006b5785c6f8e0f0e65174f989bd094f6cc47673e4ba35a9e | Python | 3,832 | 106 | from datetime import datetime
import gzip
import wget
from time import strftime
import os
from pathlib import Path
import argparse
parser = argparse.ArgumentParser(description='Make GO matrices.')
parser.add_argument('ordered_gene_list',
help='List with ordered gene IDs')
parser.add_argument('unipr... |
dc4262cde53cafcdcfa7424b2555cd5f0677d897d37806d5e0d4161fe79ee7b4 | Python | 3,833 | 109 | import numpy as np
def linear_(x, params):
a, b = params
return a*x+b
def sigmoid(x, L, x0, k, b):
return L/(1+np.exp(-k*(x-x0)))+b
def sigmoid_fit(x, y):
from scipy.optimize import curve_fit
ymin = np.percentile(y, 5)
ymax = np.percentile(y, 95)
x0 = np.percentile(x, 70)
p0 = [yma... |
f31003b321f2a4eee0f64f725f36f0a702194cb64fcb5421a288722bab702786 | Python | 3,833 | 78 | import json, re, string
import logging
from tqdm import tqdm
working_dir = '/home/jknafou/risklick_classification'
splits_path = working_dir + '/splits_v3t'
index_path = working_dir + '/index_v3'
dataset_path = working_dir + '/dataset_v3t_'
_RE_COMBINE_WHITESPACE = re.compile(r"\s+")
punctuation = string.punctuation
... |
1df9b6a1b749a49104d38905f46260395e32fd42acb0b8b6ee73b5a7d0f76ab5 | Python | 3,834 | 96 | # 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... |
6ee8f69d126ed11bcdbd55d5945d628912117094d8d9b8f1d054954117534934 | Python | 3,834 | 122 | import sys
import networkx as nx
import numpy as np
import matplotlib.pyplot as plt
from graphxai.datasets.BA_shapes.ba_houses import BAHousesRandomGaussFeatures,\
BAHousesRandomOneHotFeatures
from graphxai.datasets import BAShapes
from graphxai.gnn_models.node_classification.testing import *
# Contains GCN 1-3 l... |
e1550a5fe90f2b30afd976ac81453d46137a35a53817c9f140f7c9dea2683ff8 | Python | 3,836 | 109 | import copy
import logging
import mmcv
import random
from collections import defaultdict
from mmdet.datasets import CocoDataset, RepeatDataset
from pycocotools.coco import COCO
def build_divide_dataset(cfg, part_1_ratio=0.5, seed=520):
"""Need to change `coco.getImgIds()` output, i.e.,
`self.img... |
07099ea9ffab72f3fb5c621a545b603581ca73c55d60d4a633b640fa1bdba106 | Python | 3,837 | 104 | """
evaluator
Created by: Martin Sicho
On: 29.05.22, 18:12
"""
import concurrent
from tqdm.auto import tqdm
from drugex.parallel.interfaces import ParallelException, ParallelProcessor
class ParallelSupplierEvaluator(ParallelProcessor):
"""
Class implementing parallel evaluation of `MolSupplier` instances on ... |
7eee00735b0e33ef152d88e45d30f59e99ff7be9133e32eadab496f3d38500f3 | Python | 3,838 | 114 | from tqdm import tqdm
import numpy as np
import torch
from torch.utils.data.dataloader import DataLoader
import pickle
class TrainerConfig:
# optimization parameters
betas = (0.9, 0.999)
grad_norm_clip = 1.0
ckpt_path = None
history_path = None
num_workers = 0 # for DataLoader
def __init_... |
eced0ab2200ecf8cfaeebaa7fcedf3046cda5f17b14b1293264738eb9fbc3c3a | Python | 3,839 | 84 | import asyncio
import subprocess
import sys
import time
import pytest
from carla_cosmos.synthetic import av7_clip
from carla_cosmos_server.config import default_run_dir
from cosmos_workers.common import protocol, video
@pytest.fixture
def worker(tmp_path):
run = default_run_dir(tmp_path)
run.mkdir(parents=T... |
2340bbf7c91f1fc95181bd703c7b6430598b2a83700468275782378890eb1133 | Python | 3,840 | 102 | # 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... |
3b20127d16244b176929885d723da9900b173d1d4e4cb5c3e9efb402ac8915dd | Python | 3,841 | 120 | """
Refer to https://github.com/rosinality/stylegan2-pytorch/blob/master/calc_inception.py
"""
import argparse
import pickle
import os
import torch
from torch import nn
from torch.nn import functional as F
from torch.utils.data import DataLoader
from torchvision import transforms
from torchvision.models import in... |
599e1245d74d09ac43f4aa0be2eb945eef033640aa2e5a321e872f50f500890e | Python | 3,843 | 125 | #!/bin/python
import argparse
import glob
import os
import yaml
from array_tomography_lib import channel_file, colocalisation, colocalisation_result
CHANNEL_NAMES = ["PSD", "ALZ50", "SY38"]
CACHE_DIR = ".file_cache"
def main():
args = _parse_args()
in_dir = args.input
out_dir = args.output
config_... |
0c186ff0652e373354e58c1e3cc1d4334d2a122d5c79ea8bd0735a6530051ef8 | Python | 3,845 | 93 | import matplotlib
matplotlib.use("Agg")
from matplotlib import pyplot as plt
from sklearn.metrics import roc_curve
from sklearn.metrics import roc_auc_score
from sklearn.metrics import confusion_matrix
from sklearn.metrics import precision_recall_curve
from sklearn.metrics import jaccard_similarity_score
from sklearn.... |
4679aa19163570cc052f88bb5efc5ab2f1f6421570bb727e82be887b6a0d10d6 | Python | 3,847 | 99 | import logging
import unittest
from oaklib.datamodels.search_datamodel import SearchTermSyntax, SearchProperty
from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.datamodels.search import SearchConfiguration
from oak... |
b2dd9928571c19d24b5ce410838fe3c769971d453844b32d224032751a70f18a | Python | 3,847 | 108 | # -*- coding: utf-8 -*-
import numpy as np
from . import embed
from . import utils
class _ConventionCausality(object):
def __init__(self, embed_dim):
assert isinstance(embed_dim, int) and embed_dim > 1, \
'Embedding dimension must be integer (> 1).'
self.embed_dim = embed_dim
def... |
806f02972cf0991e93cffe2dfb186ddbc17cba5372b234389bcb5066a89ab595 | Python | 3,850 | 102 | import torch
import os
import pandas as pd
import numpy as np
import random
import pickle
from src.invalidSMILES import get_invalid_smiles
from src.preprocess import standardization_pipeline, remove_smiles_duplicates
from src.modelling import initialize_model, correct_SMILES
if __name__ == "__main__":
# set ra... |
f246d8a444d4aa4af96bb7934c39e13b5f26950f5a802f1d216de3b7e69e34db | Python | 3,850 | 130 | import argparse
import torch
from torch.nn import functional as F
import numpy as np
from tqdm import tqdm
import lpips
from model import Generator
def normalize(x):
return x / torch.sqrt(x.pow(2).sum(-1, keepdim=True))
def slerp(a, b, t):
a = normalize(a)
b = normalize(b)
d = (a... |
b565fa4088be8d1dcdf1c7402dd70cf2bfc19646d14a3c8ab882cffc95e74a8d | Python | 3,851 | 113 | # 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 a... |
62c2ed5fc442c0862c9a51ebda6a16b12413c26609642a5cf0441d96b3f5492a | Python | 3,853 | 105 | # 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... |
6dbe321d5b3134da7b041e32aff73ca40b92b6c05a19fd9fa9162e83cfda87f1 | Python | 3,854 | 128 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Optional
import sys
import warnings
from time import sleep
import pandas as pd
import requests
from Bio import Biopython... |
f5c11c47feb760a60efe5b6188fde4e35e389e39100347d4d92ac947e381aefe | Python | 3,854 | 104 | import tensorflow as tf
import numpy as np
def create_divergence_kernels():
"""
Create kernels in 3 different direction to calculate central differences
The kernels will filter out the x, y, z direction vector
Representing the gradients for each direction
"""
kernel_x = np.zeros((3,... |
2c3b6edbfbb4a0d8fda6a7259310435c5a35f998beeba4373839d8de8a428292 | Python | 3,855 | 105 | import pandas as pd
import numpy as np
from rl_analysis.util import count_transitions
from typing import Optional
def get_lagged_features(
values: pd.DataFrame,
dlight_features: list[str] = [
"signal_reref_dff_norm_rising_range",
"signal_reref_dff_norm_rising_slope",
"signal_reref_dff_... |
dd7fc1e4af93f4d6249fb50e518e05ab29e20bb0e9b8e9eaf334bd4114e2578c | Python | 3,855 | 108 | import torch
import torch.nn as nn
import torch.nn.init as init
class DnCNN(nn.Module):
def __init__(self, depth=17, n_channels=64, image_channels=1,
use_bnorm=True, kernel_size=3):
super(DnCNN, self).__init__()
kernel_size = 3
padding = 1
layers = []
layers.appen... |
1a08afe8390378b108789f40104197dc67c3ab7731d448370047360ad5dfb0cd | Python | 3,856 | 101 | """
File: Show_fastica_centriod_stability.py
Created: 2020-05-06
Last Changed: 2020-05-06
Author(s): H.H.Wiersma
Code to create distribution plot and a mask image used in the research plan
Copyright (C) 2019 H.H.Wiersma
This program is free software: you can redistribute it and/or modify
it under the ... |
28c588e5f371b559d4ee5f60a9bb39eeccd3e32c8ee3609fda7ecb694deedb06 | Python | 3,856 | 101 | import os
import traceback
import unittest
from unittest.mock import MagicMock, patch
import requests
from oaklib import get_adapter
from oaklib.constants import TIMEOUT_SECONDS
from oaklib.implementations.ncbi.eutils_implementation import (
EFETCH_URL,
REQUEST_INTERVAL,
REQUEST_INTERVAL_WITH_KEY,
)
EMPT... |
8c5b7a9e2a95aaac53eb0fe82c7478d3e10a48983e1d8a170b721fff329337b8 | Python | 3,859 | 97 | """
A set of utilities for performing loop extrusion simulations.
"""
class bondUpdater(object):
def __init__(self, LEFpositions):
"""
:param smcTransObject: smc translocator object to work with
"""
self.LEFpositions = LEFpositions
self.curtime = 0
self.allBonds = [... |
bacfdd072c654c52f855e081aced35e0573f3b2a5d97719c3709e179ee325513 | Python | 3,860 | 113 | """
This file defines the core research contribution
"""
import matplotlib
matplotlib.use('Agg')
import torch
from torch import nn
from models.encoders import psp_encoders
from models.stylegan2.model import Generator
from configs.paths_config import model_paths
def get_keys(d, name):
if 'state_dict' in d:
d = d['... |
83bc2f1ae7e4fe4d39b79c95fca6539d6d1203408b273a7e2adf7be6ab733d13 | Python | 3,861 | 96 | import json
from collections import defaultdict
import inflect
import spacy
from tqdm import tqdm
if __name__ == "__main__":
nlp = spacy.load("en_core_web_sm")
inflect_engine = inflect.engine()
with open("data/preprocess/2_unknown_2_known.json") as in_file:
contexts = json.load(in_file)
def g... |
8d2f21feef8b7827dac22b2db2c6def1f877d6e06bd11e5278308e5ad4fae6ed | Python | 3,861 | 173 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 20 21:08:56 2021
@author: N.V
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jul 20 18:47:06 2021
@author: N.V
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# not... |
b49280f5292aa56c40c3d4d8f5783935be3cf699e154d9043f7f74009f1ca78e | Python | 3,862 | 97 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
class PPO():
def __init__(self,
actor_critic,
clip_param,
ppo_epoch,
num_mini_batch,
value_loss_coef,
entropy_coef,
... |
f8b8928b37b05ecd9191d7f409cd2ab2b56f028e0e5e7783ede9616fbef6b60c | Python | 3,863 | 129 | from numpy import random
import math
import numpy as np
import matplotlib.pyplot as plt
import copy
import scipy as sp
import scipy.optimize
from sklearn.decomposition import PCA
import seaborn as sns
import pandas as pd
from sklearn.metrics import roc_auc_score
from sklearn.preprocessing import normalize
... |
14d184feb888a4fce46c559b5295d94b4f9d185e9a90c86765edd04e8ef9c819 | Python | 3,864 | 141 | import os
import cv2
import torch
import numpy as np
from PIL import Image
from dlib import cnn_face_detection_model_v1 as face_detect_model
def center_crop(im, length):
w, h = im.size
left = w//2 - length//2
right = w//2 + length//2
top = h//2 - length//2
bottom = h//2 + length//2
... |
1b95fcd3984aafd3acbf6bf488edc0664def4a51fa7721402dbc8bb9d70d4ae2 | Python | 3,866 | 130 | # -*- coding: utf-8 -*-
from .core import *
from .. import _logging as logging
import tensorflow as tf
__all__ = [
'FlattenLayer',
'ReshapeLayer',
'TransposeLayer',
]
class FlattenLayer(Layer):
"""A layer that reshapes high-dimension input into a vector.
Then we often apply DenseLayer, RNNLayer... |
3b82ccab8ff8c77a89cabc006c53687e015e8b37011629a0b99ee649cdaa7782 | Python | 3,866 | 108 | from pathlib import Path
from typing import Callable, Optional, Tuple
import matplotlib.pyplot as plt
import numpy as np
import tokenizers
import torch
import torch.nn as nn
import torch.nn.functional as F
import transformers
from accelerate import Accelerator
from matplotlib.lines import Line2D
from torch.nn.utils.rn... |
6ef6bd22f0af75a907f5f262ca57bd1895624613a83886856b5774fc94cef97c | Python | 3,867 | 113 | from typing import Tuple, List
try: # pardiso (using Intel MKL) is much faster than scipy's solver
from .mkl import spsolve_pardiso as _spsolve
except OSError: # if mkl isn't installed
from scipy.sparse.linalg import spsolve as _spsolve
import numpy as np
import scipy.sparse as sp
import jax.numpy as jnp
im... |
abb8b076688059dbd48d0a12d758abecf5a64bd84dc99cd8405d475c36aece3b | Python | 3,867 | 97 | import pandas as pd
import os
import inspect
import AIS_parameters
import AIS_import
import numpy as np
import re
fname = os.path.split( inspect.getfile(inspect.currentframe()) )[1]
##
df_vessel_types = None
df_vessel_status = None
def clean_vessel_type_str(str_):
sub_list = ['all ships of this ty... |
488021763e94293f287c5e6e6c7590f5e458bac5188b7ca361ca96bb3d27b6d7 | Python | 3,868 | 114 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the di... |
a5e60dd761fb47524f5239b5bc42b8e2abd041c88a3539a980c3d2d5d8b4d465 | Python | 3,868 | 125 | # -*- coding: utf-8 -*-
"""
Creación de un flujo de vídeo simulado
Por UDP
"""
from time import sleep
import cv2, socket, traceback, struct, sys, zlib, pickle
from sys import argv
from getopt import getopt, GetoptError
__author__="José Luis Garrido Labrador"
def help_(salida=0):
print("Ayuda sobre el emisor")
... |
797bb97b55bbc07fd83ef2d34b23b3f879186817ddc79cb01100b523eee6f6ed | Python | 3,869 | 125 | # -*- coding: utf-8 -*-
import unetsl
import unetsl.config
import pathlib
import json
class HeadConstants:
name = "name"
n_labels = "n_labels"
bits = "bits"
activation = "activation"
depth = "depth"
resampler = "resampler"
offset = "offset"
def getDefaultCerberusConfig():
unet = une... |
be1eb2c1b7a312da4ce0d7dfa9029ec3799445a4138abc932792dd09a9212ee9 | Python | 3,869 | 133 | """
.. _burgers_2d_fd_vis :
A finite difference solver for Burgers' equation in 2 dimensions
===============================================================
An intro to our loss module's finite difference utility demonstrating
its use to create a simple numerical solver for Burgers' equation in 2d.
"""
# %%
# .. raw... |
df08ce9f3766ea53d019488823243fe42e6e3831c51f8353b5a13554bf606f21 | Python | 3,870 | 79 | import json, re, string
import logging
from tqdm import tqdm
working_dir = '/home/jknafou/risklick_classification'
splits_path = working_dir + '/splits_v3'
index_path = working_dir + '/index_v3'
dataset_path = working_dir + '/dataset_'
_RE_COMBINE_WHITESPACE = re.compile(r"\s+")
punctuation = string.punctuation
punct... |
a275193f8d4728b372f09033dd59743e85f8cac8a10685a99365090f10761245 | Python | 3,871 | 170 | import matplotlib.pyplot as plt
import numpy as np
import colorcet as cc
CLASS_IND_DICT = {
"KC": 0,
"KC-1claw": 28,
"KC-2claw": 32,
"KC-3claw": 92,
"KC-4claw": 91,
"KC-5claw": 78,
"KC-6claw": 61,
"APL": 24,
"MBIN": 121,
"MBIN-DAN": 58,
"MBIN-OAN": 5,
"MBON": 172,
"... |
58483182fceb22e31ac2fbbbcb74575ccd82c13e9a065136c724875c479f3426 | Python | 3,873 | 97 | from __future__ import print_function
import sys
import os
import argparse
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision.transforms as transforms
from torch.autograd import Variable
from data import VOC_ROOT, VOC_CLASSES as labelmap
from PIL import Image
from data import VOC... |
708c2e4b7bcad661932fe75a7f8ce5cd33a0f358d44dc115ba98735d6dc7abd1 | Python | 3,875 | 93 | import pandas as pd
pd.set_option('display.width', 1000)
pd.set_option('display.max_rows', 10000)
pd.set_option('display.max_columns', 10000)
def round_value(value, binary=False):
divisor = 1024. if binary else 1000.
if value // divisor ** 4 > 0:
return str(round(value / divisor ** 4, 2)) + 'T'
... |
2f98619142859ec94295e1c9d880a4482662c4261baaddfd5aeba270addc780e | Python | 3,876 | 126 | #!/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>.
# ===========================================================================... |
141615deaef7a1f5b60aee452a2166c01f756e86944381d43037981545feec2a | Python | 3,877 | 118 | """
Description:
The script we use to prepare the directory/files needed to export
a model to the Kipoi model zoo.
Output:
Saves model.yaml, class names, and model state dictionary weights to a
user-specified output directory.
Usage:
kipoi_export.py <saved-model-pth> <class-names> <config-yaml> <o... |
e8546d60c81669b33075001230c983b887a808ce0b0a4dd351d3d0495382a0cf | Python | 3,877 | 78 | # 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... |
8aaf6c8eb61b729fd8791fa3e35e43504eb092b6caa82b975a2531d01ef93574 | Python | 3,879 | 107 | from operator import sub
import numpy as np
import h5py
import matplotlib.pyplot as plt
def rotate(u, v, w, plane, theta):
x = [u, v, w]
if plane == 1:
ax = (0, 1)
rmat = [[1, 0, 0], [0, np.cos(theta), -np.sin(theta)], [0, np.sin(theta), np.cos(theta)]]
elif plane == 2:
ax = (0, 2... |
f7e6b897afb7bcf7a5063f7208614618d1daad15fe80f94cc75cbcd9ebcbe684 | Python | 3,879 | 105 | import math
from functools import reduce
import torch
from torch import nn
import torch.nn.functional as F
# helpers
def prob_mask_like(t, prob):
return torch.zeros_like(t).float().uniform_(0, 1) < prob
def mask_with_tokens(t, token_ids):
init_no_mask = torch.full_like(t, False, dtype=torch.bool)
mask =... |
3557edbd902208de230a0d3aa8cdb342127df666663d02e967d5c37fcd713189 | Python | 3,881 | 108 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Tuple, Dict
import pandas as pd
from tmkit.topology.pdbtm.ToFastaId import toFastaId
from tmkit.topology.Phobius import ... |
428c21d702ee280424b2d20113079d98dfeb956d97c563211b2fbdad9a69a8f3 | Python | 3,881 | 102 |
"""
Created on Thu Oct 26 11:23:47 2017
@author: Utku Ozbulak - github.com/utkuozbulak
"""
import torch
from torch.nn import ReLU
from misc_functions import (get_example_params,
convert_to_grayscale,
save_gradient_images,
get_positive... |
6462cd70a709d21e5dc1f5b7c6ed6f73d828b225e8e7f001bd4668b30eddaa50 | Python | 3,881 | 128 | from typing import List
import torch
from torch.utils.data import Dataset
from .base_transforms import Transform
from ...training.patching import MultigridPatching2D
class MGPatchingTransform(Transform):
"""Wraps MultigridPatching2D to expose canonical
transform .transform() and .inverse_transform() API
... |
e6885f5e696ee7be4ad358b0f20a292bfe678885d73eb22ce7b00dc96f5f987c | Python | 3,881 | 110 | #!/usr/bin/env python
import os
import sys
import tempfile
import textwrap
import numpy as np
import polychrom.polymerutils as polymerutils
if len(sys.argv) < 2:
print(textwrap.dedent("""
Usage: show filename [start end pace]
show filenum [start end pace]
filenum is... |
429915ba1483ac04e0c7df68c496c66aa666843fd0976eb5a893f51d1a07e5c5 | Python | 3,882 | 106 | #! /usr/bin/env python3
################################
### Module to read the statistics analysis output files
##################################
import numpy as np
def ReadFixedEffect(file):
""" Read the mean estimates from a file containing the statistical analysis of the peak to peak data.
input :
... |
4b6f8d1bc23f6788cbd460571b0511bd90e3e2b0725a127d53ad68f726cc4900 | Python | 3,884 | 95 | # 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... |
46b3fd0a26db9dfeb1d080f6cfc96dc2faea7f576fdbc511d05cfc76ac1fec7a | Python | 3,885 | 109 | #!/usr/bin/env python
"""Example extract script
To extract all ROI sets in all SIMA datasets:
>> python extraction.py /path/to/sima/datasets
For help and additional arguments:
>> python extraction.py --help
"""
import os
import argparse
from sima import ImagingDataset
# Never extract ROI sets with labels that con... |
75830f26d925c3ac04555ce6c31f13b2f9cdd507a029997200b354c503ae729d | Python | 3,885 | 106 | '''
@author: orisenbazuru
'''
import torch
import torch.nn as nn
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
class RNN_Net(nn.Module):
def __init__(self,
input_dim,
hidden_dim,
z_dim,
device,
num_h... |
b38643deb594f4cc4a8b9a863611e06a8a9f9034afbc1285deba12c96296a390 | Python | 3,885 | 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... |
6d292fa48f131a0e5137c863a155a7c2e2aa208d5347c686fefdaf1e945b965d | Python | 3,886 | 115 | # 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... |
cff05efc064e422fd39c2883d7f8bd04ff1171552af360003150dae240c60c26 | Python | 3,886 | 104 | """
Title
-----
Back-propagating dSpikes
Description
-----------
An important property of biological neurons is that action potentials (APs)
initiated in the axon can invade the soma and nearby dendrites and propagate
backwards toward the dendritic tips. The transmission efficacy of these
back-propagating action poten... |
f4e258a49e5a0bf2db6d04fb5359df247aa7db8c6567ea8417d7a7b64c7f7e4f | Python | 3,886 | 111 | import os
import numpy as np
import pandas as pd
import feather
import scipy.integrate as it
from loadFile import *
def v2nm(V, calibration):
"""
This function will convert the piezoscanner voltage signal into distance.
A 20x gain is applied due to the presence of a 20x high-voltage amplifier in series wit... |
105bdc6673bcfdbcd3580f5c575456029a645e56f63d0b7a4291cb4e0869625d | Python | 3,887 | 118 | import torch
import torch.nn as nn
from torch.nn.parameter import Parameter
from torch.autograd import Variable
import torch.nn.functional as F
from utils import Config
config = Config('config/')
class GraphAttentionLayer(nn.Module):
def __init__(self, requires_grad=True):
super(GraphAttentionLayer, self... |
75077473f6464774d4862c5834ec1e5eb94aa1ab383bede817d128d3150951d4 | Python | 3,887 | 117 | # 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... |
d945113ca3c016a5f34254e8769a6a6d599e94e7d6c5a8bb198f9ea0e6c6bdbc | Python | 3,888 | 138 | import json
from os import listdir
from pathlib import Path
import numpy as np
import pymaid
from src.pymaid import start_instance
def extract_ids(lod):
out_list = []
for d in lod:
skel_id = d["skeleton_id"]
out_list.append(skel_id)
return out_list
def remove_date(string):
datestri... |
30d6fa852f9c31ef905073b287722ebeb6eb3591ea50c014706ef7d20e7e035e | Python | 3,889 | 111 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import List, Tuple
import numpy as np
import pandas as pd
class Network:
def single(
self,
interacting_df:... |
376164120a49596edcca9ed503b9bb9c7265ab31241c82fa20327681059b6357 | Python | 3,890 | 115 | # 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... |
d3392c7b9892626512cc760a6d2b3f54226b6142822d9d7346e8164ff39c15af | Python | 3,890 | 101 | from re import I
from itertools import chain
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.inspection import permutation_importance
from sklearn.preprocessing import OneHotEncoder, MinMaxScaler
from sklearn.pipeline import Pipeline
from sklearn.compose import... |
e3342999e1c23c52a858ffafc1cdc5ca5e556c3672254c84404e0cedf34d758c | Python | 3,890 | 107 | import glob
import argparse
import gzip
import os
import multiprocessing
import datetime
import sys
parser = argparse.ArgumentParser(description='Simplify psi matrix')
parser.add_argument('psi_dir', help='Directory with psi files')
parser.add_argument('outdir', help='outdir to write to')
parser.add_argument('--multipr... |
c2c4669248b1080cd9e1d229a64d5e0e4094513df88d227356851faaddb16011 | Python | 3,891 | 105 | """
This is the template script for running PBT with lfads_tf2
modified to be run with the Lorenz dataset.
Ref: https://github.com/snel-repo/autolfads-tf2/blob/main/example_scripts/run_pbt.py
"""
import shutil
from pathlib import Path
import ray
import yaml
from lfads_tf2.utils import flatten
from ray import tune
fro... |
0f7e26340e693fed2f5a1e68aad5968acb89059d59308071493f95cf7313d19d | Python | 3,893 | 107 | # 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 time
import carla
from . import SmokeTest
OUTSIDE_JUNCTION_TRAFFIC_LIGHT_XODR = """<?xml ... |
e409c33b450629cbffa11823fd02e9d22036365399d24ff3ec6bab9c6a3f2ff4 | Python | 3,893 | 90 | import torch
from mmdet.core import bbox2roi
from ..builder import HEADS, build_head
from .standard_roi_head import StandardRoIHead
@HEADS.register_module()
class MaskScoringRoIHead(StandardRoIHead):
"""Mask Scoring RoIHead for Mask Scoring RCNN.
https://arxiv.org/abs/1903.00241
"""
def __init__(se... |
c7d2ae355eaa0223522c843dbf0eb4b3ea910f85d55ee279a271992e6f2fdbd5 | Python | 3,894 | 105 | ####################################################################################################
# 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 ... |
15cea1b6ff00eb1014507d1cbc804a4e0c004917ea95db6e99a5d21df4be99e1 | Python | 3,896 | 115 | # 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... |
57645c507c4c6f89a172d0416e07235842ae8316cb2c8e98b8808c8038a423db | Python | 3,896 | 93 | import torch
import torch.nn as nn
from torch.autograd import Variable
import dni
class RNNModel(nn.Module):
"""Container module with an encoder, a recurrent module, and a decoder."""
def __init__(self, rnn_type, ntoken, ninp, nhid, nlayers, dropout=0.5, tie_weights=False, use_dni=False):
super(RNNMod... |
3930f94c90dbcb8f12287736d7527cbd27f635b4294f664c35fe8961b546f5bf | Python | 3,898 | 112 | #!/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>.
"""Example visualization of vehicle doors opening"""
import argparse
import ... |
05fa97cf021d14d651b74719c51599a2cc041999848fa0deba531094b418d000 | Python | 3,899 | 105 | """
This is the template script for running PBT with lfads_tf2
modified to be run with the mc_maze dataset.
Ref: https://github.com/snel-repo/autolfads-tf2/blob/main/example_scripts/run_pbt.py
"""
import shutil
from pathlib import Path
import ray
import yaml
from lfads_tf2.utils import flatten
from ray import tune
fr... |
e21a1c7b37597485949753480378b91f105e95dcf31d96e22340d9f00a669f38 | Python | 3,900 | 109 | # 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... |
5851e2249971971cc51f98268ab2b62e1d3350d28c2b4c044111e4edb8a470d0 | Python | 3,901 | 99 | import numpy as np
import tensorflow as tf
from roi_pooling_ops import roi_pooling
class RoiPoolingTest(tf.test.TestCase):
# TODO(maciek): add python, implementation and test outputs
# TODO(maciek): test pool_height != pool_width, height != width
def test_roi_pooling_grad(self):
# TODO(maciek): ... |
81e278bc651745f53bb7c67dc5108b96b6a87d770bbeb32a11b8634551601b0c | Python | 3,901 | 115 | # 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... |
133a6fea37c00baf44645175f085e73fc6b1203811919c28ea9810f89797784f | Python | 3,902 | 132 | #!/usr/bin/env python
import sys
import os
from distutils.dist import Distribution
if 'setuptools' in sys.modules or any(
s.startswith('bdist') for s in sys.argv) or any(
s.startswith('develop') for s in sys.argv):
from setuptools import setup as setup
from setuptools import Extension
else: #... |
b40f0a5c96f202fffd2c8193f08f6ec0d32e5ee2a239b10416a8c6cac28b239a | Python | 3,902 | 133 | # encoding: utf-8
import os
import sys
import time
import argparse
from collections import OrderedDict, defaultdict
import torch
import torch.utils.model_zoo as model_zoo
import torch.distributed as dist
from engine.logger import get_logger
logger = get_logger()
model_urls = {
'resnet18': 'https://download.pyto... |
23f8c5e1c1408450f3bc429ff5548c32dfdee0e7159c288af63555ab4df03586 | Python | 3,903 | 138 | # Copyright 2017 Google Inc. 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 or a... |
5971632d64a0f8ba30adfd856cb07553994a0cf4e46abc0ca5e2aa6bbca138a0 | Python | 3,903 | 98 | #!/usr/bin/env python
import random
import argparse
from os.path import basename, splitext
import HTSeq
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from scipy.stats import pearsonr
parser = argparse.ArgumentParser()
parser.add_argument("-c", "--chromsize", metavar="FILE", help="Index fil... |
a480d19e118fffc3309f251950ab8aa8ba3825fa334d2e9fc4499d558202f329 | Python | 3,903 | 117 | import connectome_tools.process_matrix as promat
import pandas as pd
import glob as gl
import numpy as np
# load whole brain connectivity matrix
matrix = pd.read_csv('data/Gadn-pair-sorted.csv', header=0, index_col=0)
# import pair list CSV, manually generated
pairs = pd.read_csv('data/bp-pairs-2020-01-28.csv', heade... |
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