sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
aaa03ffee3f04c670f6447201d93f2ef594e92c96ee3bcb9b68129245be79af1 | Python | 7,198 | 192 | """Convert an Alpamayo path into CARLA throttle, brake, and steering."""
from __future__ import annotations
from dataclasses import dataclass
import numpy as np
@dataclass(frozen=True)
class ControlCommand:
throttle: float
brake: float
steer: float
target_speed_mps: float
target_index: int
... |
cb49f907679685584c5194bc606e39e91d4148b9b5e9fd95bef42745e1fa73c9 | Python | 7,198 | 209 | """Implementation of the Fisher kernel for prediction studies.
See the :doc:`HMM description </models/hmm>` for further details.
See Also
--------
`Example script <https://github.com/OHBA-analysis/osl-dynamics/blob/main\
/examples/simulation/hmm_hmm-mvn_fisher-kernel.py>`_ applying the Fisher kernel
to simulated HMM ... |
e241efbe470f91a41006363efff1bd9004b5aadc679dc88d019f18d4691d8c6a | Python | 7,200 | 185 | # 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... |
24999a8fdf61bd5bea7f0fbd949ef9bcb6ce2f187aa052be0f50df4fc0039726 | Python | 7,206 | 156 | # 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... |
6c0de52905fd14d10595971dbba9c807506f50535284ae409aac2ae52a0e73a0 | Python | 7,206 | 157 | # 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... |
6b2f2d73fbb7f89792917ee59efd81cb66f7af3291bb231a98ae75100819f518 | Python | 7,208 | 219 | import os
import subprocess
from io import StringIO
import numpy as np
import pandas as pd
from scipy.spatial import distance_matrix
def parse_pdbfile(pdbfile):
file = open(pdbfile, "r")
lines = file.readlines()
file.close()
lines = [l for l in lines if l.startswith("ATOM")]
output = {}
for ... |
d002a29cc9e5a23d576c1794a96e3310697a792bcf59cdb2094cf538751115f0 | Python | 7,214 | 177 | """
The featurizers of raw text, i.e., either of Bag-Of-Words or transformer-based Language Models.
The BOW-based object (BagOfWordsBasic) should first fit to the training set (vocabulary, tokens dictionary,
random-projections matrix) and be saved as a pickled object. There you have the choice for
"""
import torch
imp... |
7d65366845e00f185c3f722a8d977aac8d996fe27c99a99296404367ce1fcb75 | Python | 7,215 | 243 | """
Training script for FNOGNO on Car CFD dataset.
This script trains a Fourier Neural Operator with Graph Neural Operator (FNOGNO)
on computational fluid dynamics data for car pressure prediction.
The model learns to predict pressure fields from geometric inputs.
"""
import torch
import wandb
import sys
from neuralo... |
cfa9a0cfbf4da702dcbf7f8dc98b0beef9a537e8e43122d23af9e45becd2396c | Python | 7,218 | 160 | import os
import re
import pickle
import subprocess
import numpy as np
from scipy.special import softmax
from scipy.spatial.distance import pdist, squareform
from data.process_label import generate_lddt_score, parse_pdbfile, get_coords_ca
def process_alphafold_model(input_model_path, alphafold_prediction_path, lddt... |
9e870753d1c86b2f7f4257ba9a98d0f55308ec1ccb9ab281a5de42e907b51ecb | Python | 7,220 | 249 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
import numpy as np
import pandas as pd
from tmkit.db.Reader import Reader as ppireader
from tmkit.structure.PDB import PDB as spdb
from tmki... |
247db0a7ae01baec3e90c676daa692917988bc75d3a3a4c93ad0f4e7ad6e5016 | Python | 7,225 | 187 | ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
## Created by: Hang Zhang
## ECE Department, Rutgers University
## Email: zhang.hang@rutgers.edu
## Copyright (c) 2017
##
## This source code is licensed under the MIT-style license found in the
## LICENSE file in the root directory of this sou... |
ce1c4b68f6d32908667a8de793aae74e8e595fde64484d7d1a8dfc7dfd33ff09 | Python | 7,225 | 177 | # 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... |
e84676d89d96bc0ff661189cb587df1a6add4b851f3cc4c6b13159817df46727 | Python | 7,226 | 176 | import astra
import numpy as np
import math as m
import matplotlib.pyplot as plt
import imageio
from pathlib import Path
from scipy import ndimage
import flexdata
class Projector(object):
'''Class performing forward projection and generation of data
:param obj: instance of Object Creator providing object'... |
f432fbe0969baa42c78848a3f57e11ddca0d19309a04b10b37769214a7c60df8 | Python | 7,226 | 166 | import torch
import numpy as np
from torch.nn import functional as F
from .resnet import *
# Implementation of DeepAccNet
class DeepAccNet(torch.nn.Module):
# Parameter initialization
def __init__(self,
onebody_size = 70,
twobody_size = 33,
protein_size... |
e78ebbaf1b0d914dae32ad7b461715c91fab25644e939567984a8f0aaeb08d87 | Python | 7,230 | 159 | #!/usr/bin/env python3
# -*- coding: utf-8 -*
"""Trimming gait data to specified length.
"""
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
import os
import glob
plt.style.use('ggplot')
plt.rcParams["axes.labelsize"] = 10
plt.rcParams["axes.titlesize"] = 14
def main()... |
0d622a9236841755b66ffadc1d6e74fd39627d7a21a598c6821a3986dce1a94e | Python | 7,235 | 177 | # SPDX-FileCopyrightText: © 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""
Pygame Display Module
This module provides a threaded Pygame display for showing camera images from CARLA.
It runs in a separate thread to avoid blocking the main application thread and
provides... |
5b2ecf89efc947fe83b176b95bac303f217fbef3e21a01ba32851a20b74c7189 | Python | 7,235 | 197 | """
Written by Nathan Neeteson.
A set of utilities for morphometry on an image and/or binary mask.
"""
import numpy as np
from scipy import ndimage as ndi
from skimage.morphology import skeletonize_3d
def crop_image_to_values(image):
# this function uses the nonzeros ndarray method to identify the indices
# o... |
7bfc477408b434fb3b631d71fe49d8995a900d7d3698cf08cd78ca12dd0a0441 | Python | 7,237 | 179 | import pandas as pd
from tqdm import tqdm
import numpy as np
from scipy.sparse import coo_matrix
import os
from torch_geometric.data import Data
import torch
from rdkit import Chem
from rdkit.Chem import AllChem
from .atom_features import get_available_features_generators, atom_features_union
import n... |
a654011b1c44eb366cf34888f627ba789829f2804df815ceeaf450cc844b826c | Python | 7,237 | 200 | """
DeepCT architecture without Sigmoid layer
for multiple cell type per position computation at once
with quantitative features (TODO: Add our names).
"""
import os
import numpy as np
import torch
import torch.nn as nn
from torch import mean
from torch.nn import MSELoss
from torch.utils.tensorboard import SummaryWri... |
9046984966f4acabab4a2636d200356468f2aa5118c7afe9321cf23f95862d68 | Python | 7,238 | 177 | """
This file contains specific functions for computing losses on the RetinaNet
file
"""
import torch
from torch.nn import functional as F
from maskrcnn_benchmark.layers import smooth_l1_loss
from maskrcnn_benchmark.layers import SigmoidFocalLoss
from maskrcnn_benchmark.modeling.matcher import Matcher
from maskrcnn_... |
cfbdd0e17439ae56bac726e1349813e54b393a7dcab11b40e96326441f21863d | Python | 7,238 | 201 | # 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... |
3dd047d1dda753fcfaca6db9130ca3f1acee8358eb6d4de55037ed80d91ac9ca | Python | 7,240 | 201 | '''
This file might work differently in the future! Don't reuse it
'''
import scipy as sp
import mesh
import myOS
import FMM.inputDat as inputDat
base_folder = 'expected_new'
# Flagellum
def write_flag():
folder_expected = base_folder + '/flagellum'
s = sp.linspace(0, 2, 10)
radius = 0.1
azimuth_... |
7a7f6220f162c72b99f74e35ed5ec344db61331c2844b7db3275f57a54641cd2 | Python | 7,243 | 209 | """
This module provides the EvaluateModel class.
"""
import logging
import os
import warnings
import numpy as np
import torch
import torch.nn as nn
from selene_sdk.sequences import Genome
from selene_sdk.utils import (
PerformanceMetrics,
initialize_logger,
load_model_from_state_dict,
)
from sklearn.metri... |
fcdeb7fb7f2bf3f9434c8012a12540ef595225d23687e83a7992bcf0d5237dfd | Python | 7,243 | 186 | # %%
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from pymaid_creds import url, name, password, token
from data_settings import data_date, pairs_path#, data_date_projectome
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
from contools import Celltyp... |
624252e6ee45d7263b71b42fbf2fdf5eda29a7cbcac54a911aa77c2c2236b187 | Python | 7,245 | 218 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
r"""
Basic training script for PyTorch
"""
# Set up custom environment before nearly anything else is imported
# NOTE: this should be the first import (no not reorder)
from maskrcnn_benchmark.utils.env import setup_environment # noqa F401 isort:s... |
c8a5c4f182cdcad07462f51075db20ed0622666a31f51bddb79f08fb773c24c4 | Python | 7,247 | 193 | # 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... |
28a0408045e39cd8fdc83b7352934cd540d2c4065c3cc2862b481a845d14371c | Python | 7,254 | 141 | #!/usr/bin/env python3
"""
File: gtex_cellmap_expression.py
Created: 2020/06/16
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Softwa... |
6541a2c10609fc198087db52e7d5869bec78f5d3f2b16995df58cc9661d25eb1 | Python | 7,256 | 210 | """This script normalizes the data from recount3"""
import argparse
from typing import Dict
import numpy as np
import tqdm
import utils
def parse_gene_lengths(file_path: str) -> Dict[str, int]:
"""Parses a tsv file containing genes and their length
Arguments
---------
file_path - The path to the f... |
3d21bfb7714a0cb728848dd9cadd6457b65942e9cbebf4d35da891a071d33f52 | Python | 7,258 | 216 | # 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... |
7cf1adcbaa501daf01f63b963c55cc9066f0eaf45365961714403ade17aa721d | Python | 7,259 | 159 | import logging
from collections import Iterator, defaultdict
from typing import Dict, List, Tuple
import networkx as nx
from oaklib.datamodels.vocabulary import IS_A
from oaklib.interfaces import MappingProviderInterface, RelationGraphInterface
from oaklib.interfaces.obograph_interface import OboGraphInterface
from oa... |
ae9018e6e22a37ec47613f2f7611c7b9d4f4ae17464ccf70549ed794883f154b | Python | 7,261 | 216 | from __future__ import annotations
from math import pi
from typing import List, Optional, Tuple, Union
from brian2.units import Quantity
class EphysProperties(object):
"""
A class for calculating various important electrophysiological properties
for a single compartment.
Note
----
An EphysP... |
151ad536101fa50cb2434e02a7e4146588ff6d3e9fc8313786209f84a163673a | Python | 7,274 | 213 | import math
import torch
from torch import nn
import torch.nn.functional as F
from neural_networks.base_models import BaseModel
CUT_OFF = {'dish washer': 2500,
'fridge': 300,
'kettle': 2000,
'microwave': 3000,
'washing machine': 2500}
MIN_OFF_DUR = {'dish washer': 1800,
... |
0e1bbbdbe90faacf21a9b98181d3703f77d98db34460702894710d962422f0b2 | Python | 7,275 | 168 | # 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... |
52868ae678ddf3536361982faf0d47017a061829fb8138bc0cf71deb17c14906 | Python | 7,275 | 184 | __author__ = 'duarte'
import sys
from preset import *
import numpy as np
"""
spike_pattern_input
- main spike_input stimulus processing
"""
run = 'local'
data_label = 'example4_spike_pattern_input'
# #####################################################################################################################... |
ec935d6ef35d516fbb90a1b2ed1c4e850b8023ef686d2b55a1ec1ac0046b7d68 | Python | 7,275 | 257 | import os
import sys
import numpy as np
import pyqtgraph as pg
from PyQt5.QtCore import *
from pyqtgraph.Qt import QtGui, QtCore
class MovablePoints(pg.GraphItem):
mouseHovered = pyqtSignal(object)
mouseDragged = pyqtSignal(object)
mouseClicked = pyqtSignal(object)
def __init__(self):
self.dr... |
fbd6f0ae747cec7484e1b2d1a46984abe209f3740ffd9d17b5618c07a978126b | Python | 7,275 | 183 | """
File: SVD_wrapper.py
Created: 2020-04-29
Last Changed: 2020-04-29
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 terms of the GNU Gen... |
95df87d4029d81fdf86a8e3df1a8f7c41f8d0148f425fbeab3cc61310d4c1505 | Python | 7,278 | 246 | from abc import ABC, abstractmethod
from random import SystemRandom
from typing import Any, Iterable, List, NamedTuple, Optional, Tuple, Type, Union
import numpy as np
hard_random = SystemRandom()
modes = ("random", "value")
def _generate_random_intervals(
dt: float, average: float, left_shift: float, right_sh... |
951c73ceb4eb36b538f609e6ada0fbc53c2f2de134f9107b98afdfb431a5b37a | Python | 7,279 | 244 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 11 10:34:36 2022
@author: alexandra
"""
import pandas as pd
import matplotlib.pyplot as plt
import scipy as sp
import numpy as np
import os
import shutil
from scipy.signal import savgol_filter
from os import path
import csv
from scipy import specia... |
97bd558fd04054ab47adde6d081ebf1ced82871ad800c16d61f0dde814699dda | Python | 7,281 | 173 | #!/usr/bin/env python3
"""List the scenarios a scenario_runner checkout can actually run.
Parses srunner/examples/*.xml directly, which is what `scenario_runner.py --list`
reads — but without importing carla or building a client, so it answers with no
server running and no PythonAPI on the path.
list_scenarios.py... |
fccebd3b412482e3351dee6f25b28f87d67fe6a8ab3af09e899c94e568797fff | Python | 7,285 | 154 | # 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... |
0c8fe311e1e984de52e4d878dc4ecb03371839f9b2fdaaf3b2ac22e63629e195 | Python | 7,286 | 179 | # SPDX-FileCopyrightText: © 2022-2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""
Projection and Coordinate Transformation Functions Module
This module provides functions for coordinate system transformations between different
reference frames used in geospatial and mapp... |
3983a3039ab09ea8b0e626dc56c2ff8e7d0f540c1c5b5df8ba38f923c94043c8 | Python | 7,287 | 169 | # 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... |
f64cc17601416120b6c88f625da197c3325a7388bc370f557f8dbd3a9432c2cc | Python | 7,289 | 216 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module with functions used for selecting subsets of similar frames to use for
finetuning.
Created on Thu Jun 6 11:04:39 2019
@author: nicolas
"""
import warnings
import numpy as np
from skimage import filters, measure, morphology
from sklearn.cluster import OPTICS... |
1b37459ef88254a8e7a0c666dd06f33d17346c89247d44381e8b82cab19396eb | Python | 7,290 | 207 | import pytest
from cropro import CropConfig
BASE_REQUIRED = {
"orig_img_path_t2w": "t2w.mha",
"seg_img_path": "gland.nii.gz",
}
def test_bp_mri_requires_adc_and_hbv():
with pytest.raises(ValueError, match="orig_img_path_adc is required for bpMRI"):
CropConfig(sequence_type="bpMRI", **BASE_REQUIR... |
3b2ebabbd594bdc1b1a3eed5e51dd6053ec4913d5fd6c90847f9846d505dfa56 | Python | 7,290 | 172 | #!/usr/bin/env python
"""
Script to build a "binary wheel" for the 'pip' Python package manager for
the LAMMPS python module which includes the shared library file. After a
successful build the script attempts to install the wheel into a system
specific site-packages folder or - failing that - into the corresponding
u... |
ff590dd0f1827939b910ff64a4d4a110b58a7c7288e4c0d7ff5a17c1cd3fc5d5 | Python | 7,291 | 219 | """
Based on ExpResNet architecture (see https://www.biorxiv.org/content/10.1101/2020.06.21.163956v1.full.pdf)
A residual architecture with a skip connection for cell type embeddings.
The forward method accepts the cell type embeddings to use during training,
as well as cell targets which select the cell types (and h... |
bdce15f8a00abcfe905edda4cbbaf3d403bf074423c570eb98ca82ed3052b43a | Python | 7,296 | 178 | import csv
import os
import pandas as pd
import tqdm
from sklearn.model_selection import train_test_split
import numpy as np
import typing
import abc
import random
from dataprocessing.filters import feature_filter
import math
import pickle
T = typing.TypeVar("T")
class BaseModel(typing.Generic[T]):
def __init__... |
a1f7d81ea49c1dfe6eb27e99925cedd57bbd36b094f5967abf8bd7c9f5f7bd70 | Python | 7,301 | 189 | """
tests
Created by: Martin Sicho
On: 18.05.22, 11:49
"""
import tempfile
from unittest import TestCase
import pandas as pd
from drugex.data.corpus.corpus import SequenceCorpus
from drugex.data.corpus.vocabulary import VocSmiles, VocGraph
from drugex.data.fragments import FragmentPairsEncodedSupplier, SequenceFragm... |
0e1b113ff1634680056ec8d2307eb4eeb355f62b4abee6ab3fdfdd60cac5478a | Python | 7,303 | 254 | from typing import NamedTuple, Optional, Tuple, Union
import numpy as np
from cgtasknet.tasks.reduce.dm import DMTaskParameters
from cgtasknet.tasks.reduce.reduce_task import (
_generate_random_intervals,
ReduceTaskCognitive,
)
class CtxDMTaskParameters(NamedTuple):
dm: DMTaskParameters = DMTaskParamete... |
62c0611e9b6bb9c7dcf7c9ce0e1ace45808d7986440059275bc538a2c4bc66d2 | Python | 7,303 | 217 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init
import numpy as np
from unet import *
from utils import *
def weight_init(m):
if isinstance(m, nn.Conv3d) or isinstance(m, nn.Conv2d):
torch.nn.init.kaiming_normal_(m.weight.data)
if m.bias is not None:
m.bias.data.fill_(... |
68a547a70a3f6def5d5626ec22613c732b78f753456ccfd028937c54b2b84b60 | Python | 7,303 | 104 | import argparse
import os
from util import util
import torch
class BaseOptions():
def __init__(self):
self.parser = argparse.ArgumentParser()
self.initialized = False
def initialize(self):
# experiment specifics
self.parser.add_argument('--name', type=str, default='people', hel... |
07bc9babf1a760445dfc2eed91c318e5f2a25cac174a6761fccf56f18b9e8f31 | Python | 7,304 | 238 | # 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... |
8a7ea5f8abcefa78b330ee8e2831861c461ea12e1cfa1bc7151411ebf37d3bb7 | Python | 7,305 | 140 | __author__ = 'duarte'
from modules.parameters import ParameterSet, extract_nestvalid_dict
from modules.input_architect import EncodingLayer, InputNoise
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.analysis import single_... |
052cbfe2f837980b543ad4f34063183e95d9f8ce23e99da3f4f19aaec79e6211 | Python | 7,306 | 185 | import numpy as np
import torch
import torch.nn.functional as F
from torch import nn
from torch.nn import Linear, Conv2d, BatchNorm2d, PReLU, Sequential, Module
from models.encoders.helpers import get_blocks, Flatten, bottleneck_IR, bottleneck_IR_SE
from models.stylegan2.model import EqualLinear
class GradualStyleBl... |
5d4a2afcbc5c543531053179d1764b5e134f1593fce6b8979f15af5019780f6c | Python | 7,308 | 148 | """
Modules that handle computation of fitness. This file can contain multiple modules.
"""
import os
import numpy as np
import core.settings as CoreSettings
import core.system as System
import core.gromacs as Gromacs
import core.gromacs_commands
import user.usersettings as UserSettings
def module_c... |
aac23d65e204ebeae174e6b2a435895501cb07f5cb39893cbede44e2d4180980 | Python | 7,316 | 247 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
604e4f1a2e640c995a311929e0b3d0878bdabfc7a90cc02de8a372be48149ae7 | Python | 7,318 | 243 | __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, Dict
from tmkit.id.Fasta import Fasta as idfasta
from tmkit.id.PDB import PDB as idpdb
from tmkit.topology.p... |
122fbe64829b100ba06dcce61309239f7958bfc90d3421968896ba8db8a5199a | Python | 7,320 | 186 | #!/usr/bin/env python
import random
import torch
from torch.optim import Adam
from drugex import utils, DEFAULT_DEVICE, DEFAULT_GPUS
from torch.utils.data import DataLoader, TensorDataset
from tqdm.auto import tqdm
from drugex.logs import logger
from drugex.training.explorers.interfaces import FragExplorer
from druge... |
1a4ab03a696c3bc560b16862cbb164f951fae41e6f5a61e32c00b548e21722a6 | Python | 7,326 | 172 | #Copyright (C) 2019 Soeren Lukassen
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#This program is distributed in the h... |
5633eb46ab3c496a74e6c79e6203c580e8ce1cfcb1802413e5c02680f4e49bae | Python | 7,329 | 232 | # -*- coding: utf-8 -*-
"""Data generation and anomaly generation."""
import collections
import itertools
import random
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from gstools import SRF, Gaussian
__author__ = ["KatieBuc"]
def pivot_dataframe(df):
df = df.pivot(index="t", columns="i... |
f6409b08842d4d42ca936d2ad8c40dfdf6639d0f4bb85b9405b0a1b03e730d26 | Python | 7,329 | 202 |
"""
2021/11/30
Plot comparisons of LE_dim
"""
import os
import numpy as np
import pandas as pd
from sklearn.decomposition import PCA
import umap
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.model_selection import StratifiedKFold
from siVAE import uti... |
a25af46e4e3b60be3ef5829bd08e53bad6f8f0d23addbb8899d8561f5cb0bf11 | Python | 7,334 | 238 | from typing import NamedTuple, Optional, Tuple
import numpy as np
from cgtasknet.tasks.reduce.reduce_task import (
_generate_random_intervals,
ReduceTaskCognitive,
ReduceTaskParameters,
)
class RomoTaskParameters(NamedTuple):
dt: float = ReduceTaskParameters().dt
trial_time: float = 0.25
ans... |
be2b6f96f86c2018221b69534d3f1f873a8290c79f821822e4fc288aefa82d29 | Python | 7,335 | 197 | import numpy as np
import torch
from ..builder import BBOX_CODERS
from .base_bbox_coder import BaseBBoxCoder
@BBOX_CODERS.register_module()
class DeltaXYWHBBoxCoder(BaseBBoxCoder):
"""Delta XYWH BBox coder.
Following the practice in `R-CNN <https://arxiv.org/abs/1311.2524>`_,
this coder encodes bbox (x1... |
6460ca3d28f9f18cb85af5dadbb3c0081dd3c18edf02c11e949bb2bfa2033c6b | Python | 7,337 | 141 | import plyfile
import argparse
import torch
import numpy as np
import skimage.measure
import scipy
import mrcfile
import os
N_CHANNELS = 22
def create_samples(N=256, voxel_origin=[0, 0, 0], cube_length=2.0):
# NOTE: the voxel_origin is actually the (bottom, left, down) corner, not the middle
voxel_origin = ... |
0bfd86b3de034abc80444863ce488ae2a0ae3e62fbfd45e06b2d38b0010aab2f | Python | 7,338 | 191 | # 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... |
b41b780eaf4f67c5566929a4373fef60b8fab547115228e03033778f469487c7 | Python | 7,342 | 148 | import argparse
from pathlib import Path
import torch
from torch.utils.data import DataLoader
from torchvision import transforms
from dataloading.nvidia import NvidiaDataset, Normalize, NvidiaCropWide
from dataloading.ouster import OusterCrop, OusterNormalize, OusterDataset
from metrics.metrics import calculate_open_... |
7dcbc6cd72c9b9227ecd9f9ece16bdc25dfcf512e7ba80da2cd3dd010c901f5f | Python | 7,343 | 219 | import torch.nn as nn
import torch.utils.model_zoo as model_zoo
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152']
model_urls = {
'resnet18': 'https://download.pytorch.org/models/resnet18-5c106cde.pth',
'resnet34': 'https://download.pytorch.org/models/resnet34-333f7e... |
9592da11c8bf6070742cf9719417318932f000f1b7b2cc57ff65696517c2974a | Python | 7,345 | 173 | """
==========================================
Using cloudknot to run pyAFQ on AWS batch:
==========================================
One of the purposes of ``pyAFQ`` is to analyze large-scale openly-available
datasets, such as those in the
`Human Connectome Project <https://www.humanconnectome.org/>`_.
To analyze thes... |
1bf19b168a21d66c721aadc08c1f1e3380a247cd50a544ae707038839317a197 | Python | 7,346 | 227 | import sys
import itertools
import collections
from debarcer.utilities import edit_distance
"""
Adapted from https://github.com/CGATOxford/UMI-tools/blob/master/umi_tools/network.py
(Retrieved March 21, 2018)
"""
sys.setrecursionlimit(10000)
def breadth_first_search(node, adj_list):
searched = set()
queue... |
d75e96b8812813d2e4843f2dac355c8d4b5327075bf6ea211437642eb3312f95 | Python | 7,346 | 203 | from torch import nn
from torch.autograd import Function
from torch.autograd.function import once_differentiable
from torch.nn.modules.utils import _pair
from ..utils import ext_loader
ext_module = ext_loader.load_ext(
'_ext', ['deform_roi_pool_forward', 'deform_roi_pool_backward'])
class DeformRoIPoolFunction(... |
e336036cd132f31a8a9eb53bbce1643cba96326474bb1d8a4f4a7102031b023a | Python | 7,346 | 223 | import multiprocessing as mp
from functools import partial
import numpy as np
import elephant.statistics as spkstat
from tqdm import tqdm
from pathos.multiprocessing import ProcessingPool as Pool
from elephant.kernels import GaussianKernel
from neo.core import SpikeTrain
from quantities import ms
from sklearn.base im... |
8c9974b62f4e51fcd183212102422232402c2e158fd39616697259da6b695b39 | Python | 7,351 | 187 | import numpy as np
import torch
import torch.nn as nn
from mmcv.cnn import kaiming_init, normal_init
from mmcv.ops import Conv2d, Linear, MaxPool2d
from torch.nn.modules.utils import _pair
from mmdet.core import force_fp32
from mmdet.models.builder import HEADS, build_loss
@HEADS.register_module()
class MaskIoUHead(... |
bf064ba6db2ca659e5263edb04ced001b2dfaf5eba52a588f944d6ac5c67d251 | Python | 7,354 | 300 | # %% [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... |
04bd08e740aa82d735f1d8450a2bebcf21243f3dfcca06c41604960691e50dee | Python | 7,356 | 205 | # 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... |
9197585bdc2362b005a75bf9959cee336482a5579662a7889aab0b9ed43def60 | Python | 7,356 | 155 | import torch
import sys, os, json
import warnings
warnings.filterwarnings("ignore")
import nltk
nltk.download('punkt')
sys.path.append("..")
from torch_geometric.utils import to_dense_adj
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
class Cache_GNN_Embeds():
def __init__(self, confi... |
4d90019bf839ca1860a363a18548ab60170db788c24035208bf705615d5e965a | Python | 7,363 | 197 | import numpy as np
import torch
from ..builder import BBOX_CODERS
from .base_bbox_coder import BaseBBoxCoder
@BBOX_CODERS.register_module()
class DeltaXYWHBBoxCoder(BaseBBoxCoder):
"""Delta XYWH BBox coder.
Following the practice in `R-CNN <https://arxiv.org/abs/1311.2524>`_,
this coder encodes bbox (x1... |
6f68a7cc16849d2b1e23ff1141a9919b33d4b5c00e09d7f05d118ee52646ea2c | Python | 7,363 | 191 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
#%%
import sys
sys.path.append("/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/")
import pandas as pd
import numpy as np
import connectome_tools.process_matrix as promat... |
bc9130cf5ec3b9917f2d2a79c61c1079136ad7f9193a842b8bb8774bddeb88fd | Python | 7,363 | 280 | """Train DyNeMo on Nottingham movie data.
"""
print("Setting up")
import pickle
import numpy as np
import os.path as op
from os import makedirs
from osl_dynamics import analysis, data, inference
from osl_dynamics.models.dynemo import Config, Model
from osl_dynamics.utils import plotting
#%% Settings
# GPU settings
... |
c8d276f637c8cb116a9d93da45c48234fb873b3bc4a69b39caa136d410fe7c6b | Python | 7,363 | 197 | # 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... |
798f8e1f898b2cbac3b7d6dfb07293f103e4a646bf2fe58b5c435308216d2fb5 | Python | 7,364 | 225 | import git
import logging
import os
from bisect import bisect
from datetime import datetime
from logging import config
from typing import Dict
class LevelFilter(logging.Filter):
"""
LoggingFilter used to filter one or more specific log levels messages
"""
def __init__(self, level):
self.__l... |
76268505b7a3b1d1132484ea3521f0b95c2708d85ea4129be6727ab266e10771 | Python | 7,369 | 240 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import math
import random
import copy
from keras.datasets import mnist,cifar10
from globals import EPSILON
def get_unique_examples(train_x, train_y, N):
# When working with minimal data, get as representative examples as possible
ex_per_class =... |
4954b66425b2c5d06503e28011c8711dd08821000fbf0e3c6b6f5cefaaaaf4e9 | Python | 7,375 | 201 | #!/usr/bin/env python3
# encoding: utf-8
# @Time : 2018/6/17 上午12:43
# @Author : yuchangqian
# @Contact : changqian_yu@163.com
# @File : seg_oprs.py
from collections import OrderedDict
import numpy as np
import torch
import torch.nn as nn
class ConvBnRelu(nn.Module):
def __init__(self, in_planes, out_plan... |
501bbe8ab43d968827f9c90f25d0be10616dd430d6ad07d331bb7592bee10163 | Python | 7,376 | 171 | # -*- coding: utf-8 -*-
'''
@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 neural_network_architecture
import features_extraction
import torch.nn as nn
import torch
from torch import LongTensor, FloatTensor
import ... |
8e997507c1307ce8fab00948cf1586db561ff3063dfd5f3eb98e615d357b08da | Python | 7,376 | 213 | #%%
import sys
sys.path.append('/Users/mwinding/repos/maggot_models')
from pymaid_creds import url, name, password, token
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
# allows text to be editable in ... |
0e21847086ca2db1ef489f9411f596840776a5b1e28842ddfe5a53d985b690b1 | Python | 7,379 | 173 | import csv
import gzip
import os
import sys
import tempfile
import unittest
from pathlib import Path
from shutil import copyfile
try:
from gilda.grounder import Grounder
from gilda.term import Term
have_gilda = True
except ImportError:
have_gilda = False
from oaklib.datamodels.text_annotator import T... |
9ec25d711e32df58f226ec687f5f376525fa21d12e5435214a660b400dbf39ab | Python | 7,379 | 135 | # 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... |
61c0854f1c848dfb20a52a833ae195d142701a707d8e1dbd365e08aa0b5697c7 | Python | 7,383 | 157 | # 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... |
1496d6c73bd9cbe1e0c7a6a1fddacab5bf881314249eac66c938f8354f4dcb40 | Python | 7,386 | 228 | import os
import sys
import torch
import torch.nn as nn
import math
from lib.nn import SynchronizedBatchNorm2d
try:
from urllib import urlretrieve
except ImportError:
from urllib.request import urlretrieve
__all__ = ['ResNet', 'resnet18', 'resnet50', 'resnet101'] # resnet101 is coming soon!
model_urls = {
... |
8f1082abc5d39c78d5f45c8ad86cbd739370c893cf3ad2922e334a17a9cc6007 | Python | 7,387 | 158 | # This script is used to calculate STRUCTURAL uncertainty for the smos-smap NN, and the corresponding mean ans std, as well as some other auxiliary data such as correlations, rmse, sliced and grouped data for plots
# input files: NNsmossmap_smos_output_ver1.pkl to ver7.pkl,
# NNsmossmap_overlap_output_ver1.pkl to ver7... |
f9aac4dd464fd1defefa5ad6437934fc7fc57a96fc1b9b2b21e2d56c9900be86 | Python | 7,390 | 219 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
05e7b4d63520ef3e4d1411f1fba492da2c06f3700fc6012f04291a3a26e5c66a | Python | 7,394 | 152 | """
=============================================
BabyAFQ : tractometry for infant dMRI data
=============================================
The following is an example of tractometry for infant bundles. This example and
resulting pyAFQ support for pediatric bundles was inspired by and largely due
to the work of Grothee... |
a0d79a467e8380bab92a8386d9db695f015a3667e67afb646d6c98d9bfe6d10c | Python | 7,394 | 193 | # 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... |
0d8a789c41434f844a3c835caeb47289c8bb842102c407a3304493138bf2057c | Python | 7,395 | 173 | # -*- coding: utf-8 -*-
'''
@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 neural_network_architecture
import features_extraction
import torch.nn as nn
import torch
from torch import LongTensor, FloatTensor
import ... |
34cbe5b741fb5449315c229486f8b52bac8aab6e381c4b37458544e08764e43a | Python | 7,398 | 247 | import torch
import torch.nn as nn
import torch.nn.functional as F
from utils.function import FakeQuantize
from math import e, pow
# 计算S和零点
def calc_ScaleZeroPoint(min_val, max_val, num_bits=8):
n = num_bits - 1
qmin = - 2 ** n
qmax = 2. ** n - 1.
# S=(rmax-rmin)/(qmax-qmin)
sca... |
0f2e20d7f05bd4c64e6335e3e1fac8f74ad8fc4091b5bf74efe3bbd6dfb1673e | Python | 7,400 | 266 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
1509735f9840b81acef4b48b87069bdb671d162856805d862b83f58b7110290a | Python | 7,400 | 174 | r"""
Polymer simulations with CorrelatedNoiseIntegrator
--------------------------------------------------
This is a sample python script to run a polychrom simulation with the `CorrelatedNoiseIntegrator' custom integrator
in polychrom.contrib.integrators. This integrator is used to simulate a polymer where the Browni... |
65f87cdc4f4a27b0c76de86655205b352d1a0e2c3d1633910183f54b1b6729e0 | Python | 7,406 | 191 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import bisect
import copy
import logging
import torch.utils.data
from maskrcnn_benchmark.utils.comm import get_world_size
from maskrcnn_benchmark.utils.imports import import_file
from . import datasets as D
from . import samplers
from .collate_b... |
adcc281e4da91a14e9c0b38d7b7ed1522079be08aece748c5da5f6ed4112f679 | Python | 7,407 | 255 | from __future__ import division
from builtins import next
from builtins import range
from past.utils import old_div
import os
import itertools as it
import errno
from distutils.version import LooseVersion
import numpy as np
try:
from bottleneck import nanmax
except ImportError:
from numpy import nanmax
try:
... |
3f28f3fb787422f101a5d921ef9b768228d78539091243bab6e3e370a238f54e | Python | 7,409 | 192 | """
File: inter_eqtl_celltype_details.py
Created: 2020/05/20
Last Changed: 2020/06/19
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 Foundat... |
65e7421f1776217cfa0668dd11fedc45f8b3ac7862ae8a738baab547f4db1eee | Python | 7,414 | 189 | # 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... |
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