sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9a0032478b056538e625f3991a09c684ddbd51400989413be2ef39f1b26b02cf | Python | 3,616 | 110 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 17:03:58
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 19:19:26
Description:
'''
import cv2
import torch
import fractions
import numpy as np
from PIL import Image
import torch.nn.functional as F
from torchvision import transforms
from mode... |
f481c99fbb8db97e78f8fac7d76c22eb6ea522f73155cac4e1b6169e9aeb1c29 | Python | 3,616 | 97 | import os
import sys
from types import ModuleType
from typing import Optional, Tuple
import numpy as np
from ..base import DatabaseBase, ALL, load_fids
########################################################################
class Database(DatabaseBase):
""""""
fids = load_fids(os.path.join(os.path.dirname(... |
20a91db392af9d929b044e049844a24959d6e8c68420dc224d94962a19c6200f | Python | 3,617 | 117 |
"""
2021/11/30
Plot comparisons of zv_recon_scale
"""
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 im... |
c840177327c00fcf5e1cb8b3daa77b3d1803b58d2f9c816c6054f9e418ee2622 | Python | 3,618 | 101 | #!/usr/bin/env python3
"""
File: merge_results.py
Created: 2020/07/09
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 Foundat... |
e2623bc714267516af08a4ef44aae7114dd4c0fc8b9a06fac185a879297948d2 | Python | 3,619 | 104 | # 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... |
7b052d64481aee4ad12e78675b09b1b032aed086a6c087286a8cbb4b0d423739 | Python | 3,620 | 110 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 17:03:58
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 19:19:43
Description:
'''
import cv2
import torch
import fractions
import numpy as np
from PIL import Image
import torch.nn.functional as F
from torchvision import transforms
from mode... |
d901471e86b8624d10e8e5e3fcf31b146e3cd8475e929e6dc636685e4cdc322a | Python | 3,621 | 109 | #!/bin/python
import os, shutil, sys, subprocess
import datetime
import argparse, zipfile, glob
parser = argparse.ArgumentParser()
parser.add_argument('--zip', action='store_true')
parser.add_argument('--prune-torchlibs', action='store_true')
args = parser.parse_args()
os.environ['DO_NOT_RELOAD'] = 'true'
from ba... |
6e12ffbe078e22033ea2c83fbf08b784c2dfc5de34941b018e03e1789ee96876 | Python | 3,622 | 112 | from __future__ import annotations
import logging
import os
from typing import TYPE_CHECKING, Iterable, List
from logging import Logger
from palm_tools.data_structure.trackset import TrackSets
from ..data_structure.trackset import TrackSet
from abc import ABC, abstractmethod
import json
from tqdm import tqdm
from tqdm... |
5bf185c6e2557adf5b4994892105b3c2a5d562fe92080fecc056643c8207fb9f | Python | 3,625 | 87 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Variational Animal Motion Embedding 1.0-alpha Toolbox
© K. Luxem & P. Bauer, Department of Cellular Neuroscience
Leibniz Institute for Neurobiology, Magdeburg, Germany
https://github.com/LINCellularNeuroscience/VAME
Licensed under GNU General Public License v3.0
"""
... |
8afd8eeedd0c0e3bf9b5e42f75d8d123f6edf18347e0e009b9ce104842c58eb0 | Python | 3,626 | 104 | import os.path as op
import numpy as np
import numpy.testing as npt
import nibabel as nib
import nibabel.tmpdirs as nbtmp
from dipy.core.geometry import vector_norm
import dipy.core.gradients as dpg
import dipy.data as dpd
from dipy.io.gradients import read_bvals_bvecs
import AFQ.utils.models as ut
from AFQ.models ... |
92d432008ce3f618168145e0f7f181ef01b4cd4412ffb5eb544b27e277f933d3 | Python | 3,627 | 104 | # coding=utf-8
# 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 ... |
aabc750457a82544c1dc4e6ef1381d3d8aa4c54ccbf0e4c49731ac3bdf45ff7c | Python | 3,627 | 97 | import tensorflow as tf
from tensorflow.keras import backend as K
import matplotlib
matplotlib.use('agg')
class RESNET:
def __init__(self, input_shape, nb_classes, verbose=False, build=True, is_train=True):
if build:
self.model = self.build_model(input_shape, nb_classes, is_train)
... |
4dfd58c72979f6ddf79b301cdb42996f57878746a6b08d2348a61bb03dfcec99 | Python | 3,628 | 93 | # 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... |
747844b351d60348860b8be7f08abca27245f9303082e5cbced5c5cdf16cc756 | Python | 3,629 | 95 | import torch
from mmdet.core import bbox2result, bbox_mapping_back, multiclass_nms
from ..builder import DETECTORS
from .single_stage import SingleStageDetector
@DETECTORS.register_module()
class RepPointsDetector(SingleStageDetector):
"""RepPoints: Point Set Representation for Object Detection.
This de... |
18922f1fb266297fa748ca6381481eba6107f844db99680971312683b146e76b | Python | 3,630 | 96 | import numpy as np
import scipy.ndimage as nd
import torch
import torch.nn as nn
import torch.nn.functional as F
from engine.logger import get_logger
logger = get_logger()
class SigmoidFocalLoss(nn.Module):
def __init__(self, ignore_label, gamma=2.0, alpha=0.25,
reduction='mean'):
supe... |
7266ffbf99da395d4670bb52df35626d3c1ee1486571f8ee36146a8b136c4359 | Python | 3,630 | 86 | #! /usr/bin/env python
# Copyright 2019 Ashish Arora
# Apache 2.0.
"""This script splits a kaldi (text) file
into per_speaker per_session reference (text) file"""
import argparse
def get_args():
parser = argparse.ArgumentParser(
description="""This script splits a kaldi text file
into per_sp... |
a41908400aad46719c93f418914f3bc4e90beb1f215ac7313c141abd3985ae74 | Python | 3,630 | 106 | """
Change CONFIG class which reflecting learning hyper parameter (etc., meta-prior, the number of neural units). The detail of CONFIG class was written in `config.py`.
"""
import time
import os
from datetime import datetime
from config import ConfigSoftmax as CONFIG
from analysis.analysis_tutorial import analyze_tut... |
bb8e90ce20d70cf0129f39e7e8208d55774454e542aeeef7dd0e8310079f2664 | Python | 3,630 | 112 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
import shlex
# from python 3.3 source
# https://github.com/python/cpython/blob/master/Lib/shutil.py
def which(cmd, mode=os.F_OK | os.X_OK, path=None):
"""Given a command, mode, and a P... |
1fa8ada8d4850968bb288757cec892a5efa8223d5e853181d76e928ed705a927 | Python | 3,632 | 113 | import os
import shutil
# from libtiff import TIFF
from scipy import misc
import random
import cv2
import numpy as np
# def tif2png(_src_path, _dst_path):
# """
# Usage:
# formatting `tif/tiff` files to `jpg/png` files
# :param _src_path:
# :param _dst_path:
# :return:
# """
# tif ... |
fe492195c2afed66a35d2a6bd37b4174570a4f2bbf39de5c3e742e8ab6265f63 | Python | 3,632 | 118 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
2511d9c37460b36e9545b89c9e3be1125d82bc55363cb428cdfcac4ae4f25feb | Python | 3,633 | 103 | from brainrender import Scene
from brainrender.actors.streamlines import Streamlines
import pandas as pd
import json
import glob
import re
from paper.figures import INSET # removes the scale bars?
###
# a few parameters / options
# a few parameters / options
interValue = True
saveScreen = True
animalName = "CR_transe... |
5c054a62cca62b2f60121dbedd10b6251611c86d64cc22e325838cf8eac5527a | Python | 3,633 | 92 | #!/usr/bin/env python
#title :train.py
#description :Network for MR-tod
#author :Zifei Liang
#date :2022/05/22
#usage :Network for Deep learing from MRI to TOD
#python_version :3.6
# import sys
# positionOfPath = 1
# # sys.path.insert(positionOfPath, 'R:\zhangj18lab\zhangj1... |
aac9441c55da5ef405dd95d00e3f20d3d54d7d2591adfa9eca10afc8d20d1a8d | Python | 3,633 | 112 | import mne
import evoked as erp
import stats as st
import numpy as np
import GrandAverage as ga
import matplotlib.pyplot as plt
import sys
import datetime
import os
import fnmatch
import pandas as pd
import fnmatch
from mne.channels import find_ch_connectivity
from scipy import stats
from mne.stats import... |
02c85f8e0b0d9215a82d77d8a9771d3ffeb5a546be4db07308c5d5fa3f6ac6ca | Python | 3,634 | 124 | import argparse
import matplotlib.pyplot as plt
import os
import numpy as np
import torch
from tqdm import tqdm
import pdb
from sklearn import metrics
from torch.autograd import Variable
from loader import load_data
from model import TripleMRNet
def get_parser():
parser = argparse.ArgumentParser()
parser.ad... |
27de91eaf5367a0dea9064b1ef0120c23cae8209004f9115808ef9d39243b7c2 | Python | 3,634 | 85 | import os
from copy import deepcopy
import argparse
area_report = "report_area >> %/rpt/&_area.rpt\n"
timing_report = "report_timing -path full >> %/rpt/&_timing.rpt\n"
power_report = "report_power >> %/rpt/&_power.rpt\n"
analyze = "analyze -format verilog {%/verilog_file/&.v}\n"
elaborate = "elaborate &\n"
... |
7168b327898f1c4b2c9bd7861594978cc91b89d79cdeb87c7f54970eceeea64f | Python | 3,634 | 127 | import numpy as np
import pandas as pd
import pymaid
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
import navis
volume_names = ["PS_Neuropil_manual"]
def rgb2hex(r, g, b):
r = int(255 * r)
g = int(255 * g)
b = int(255 * b)
return "#{:02x}{:02x}{:02x}".format(r, g, b)
def simple_plot_neur... |
4147fc7af2867d5c77a467e9e396f2a3fa0885064a3396dc1252e184af68a77e | Python | 3,635 | 93 | # 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... |
57d8f5d1e74827f776ee29d93d206e9d02071b8ea7cf15e7becfac5a879a8e5e | Python | 3,635 | 67 | # 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... |
115c3fba3c0a87dcaf6cce234cbd922da9156708b28d1fb892daeeac8ed4ba87 | Python | 3,637 | 149 | # %%
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from src.data import load_maggot_graph
from src.hierarchy import signal_flow
from src.data import load_palette
from src.io import savefig
from pathlib import Path
from src.visualization import set_theme
set_theme()
save_path = Path("ma... |
455fb6bb3d17ebd7858dc448069577da20bbdab41b787c046b3175b4a013961d | Python | 3,637 | 128 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from .bounding_box import BoxList
from maskrcnn_benchmark.layers import nms as _box_nms
def boxlist_nms(boxlist, nms_thresh, max_proposals=-1, score_field="scores"):
"""
Performs non-maximum suppression on a boxlist, with s... |
ec1ec75b53639391a2e81291bf71589ea4353db68cf01adfe952962e0ab76954 | Python | 3,637 | 103 | __author__ = 'jieqing jiao'
import numpy as np
from . import kt
import matplotlib.pyplot as plt
from scipy.signal import convolve
from scipy.interpolate import interp1d
from scipy.io import savemat
def make_basis(inputf1, dt, beta_lim=[10e-6, 10e-1], n_beta=128, beta_space='log', w=None, k2p=None, fig=False):
... |
d851f8fa4f45d7e3537ff3adaca8f78f0bce799c9c80912dd73c1fd298d05549 | Python | 3,638 | 98 | #! /usr/bin/env python
# Copyright 2019 Vimal Manohar
# Apache 2.0.
"""This script converts an RTTM with
speaker info into kaldi utt2spk and segments"""
import argparse
def get_args():
parser = argparse.ArgumentParser(
description="""This script converts an RTTM with
speaker info into kaldi u... |
e1fad94b061a0935fdc0b73b05a74862d30b07e8f4875c7a0070f7ffa5519a46 | Python | 3,640 | 129 | import argparse
import pickle
import torch
from torch import nn
import numpy as np
from scipy import linalg
from tqdm import tqdm
from model import Generator
from calc_inception import load_patched_inception_v3
@torch.no_grad()
def extract_feature_from_samples(
generator, inception, truncation, truncation_laten... |
ef762851a16befb5e98dbb78d1110ff0b2c5ec3c2be403123c0b78057bc57b1e | Python | 3,640 | 76 | import numpy as np
from sklearn.linear_model import LinearRegression
import warnings
import pandas as pd
from typing import Union
from src.util import susi
def approximate_filters(target_filters: str, source_filters: str, optical_system_parts=None,
normalize: bool = True) -> np.ndarray:
"... |
14c5c41fb1488f6e3300898b02e3b13bd618a27bcf22701a7ccf823eeb483271 | Python | 3,641 | 113 | # 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... |
b852aa820075d8d84e02110f2a4ad1692c2b8ca3ee987e7320ced78707f94f9a | Python | 3,641 | 146 | # -*- 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
# note that this must be executed before 'import numba'
os.environ['NUMBA_DISABLE_INTEL_... |
22cac0d26b099f815067eb1d766c8bf6089e5bde04d988bc902078c66821859f | Python | 3,644 | 100 | #!/usr/bin/env python3
import sys
def hex_to_decimal(utf8_string):
assert(len(utf8_string) == 3)
hex_dict = {}
char_list = ["0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "A", "B", "C", "D", "E", "F"]
value_list = [0, 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15]
for key, value in zip (char_list, value_... |
c846f7fc9545f4792738a250b7c3a41f628360929b2424e3f8e107d885eed864 | Python | 3,644 | 73 | import os
import pickle
import shutil
import torch
import argparse
import numpy as np
from biopandas.pdb import PandasPdb
from data.loader import expand_sh
from data.process_label import generate_dist_diff, generate_lddt_score, generate_coords_transform
from feature import create_basic_features, get_base2d_feature
fr... |
81449daf77ac4994d2387c87e5aca5df97d650c413394ceb4a1c6a6a1c239515 | Python | 3,645 | 71 | ###########################################################
## ccAF: scvelo_analysis.py ##
## ______ ______ __ __ ##
## /\ __ \ /\ ___\ /\ \/\ \ ##
## \ \ __ \ \ \___ \ \ \ \_\ \ ##
## \ \_\ \_\ \/\__... |
d4f39afad6cee318520efcf3a3443b57ce0b6be3ed3f107001bac99d124182ef | Python | 3,645 | 93 | """Fit a standard EEG montage to the MNI152 standard brain.
If we don't have digitised electrode positions or a structural MRI, we can
use a standard montage and a standard brain to source reconstruct EEG data.
However, the electrodes of a standard montage don't sit on the scalp of the
standard brain.
The coregistrat... |
297cbbc2f4b5a91114e42c31d1f4978ef7bae0b7179aa7407ded37fba3c23f1c | Python | 3,647 | 108 | import torch
import torch.nn as nn
from torch import Tensor
from torch_geometric.nn import MessagePassing
from typing import Tuple
def extract_step(model: nn.Module, x: Tensor, edge_index: Tensor, detach: bool = True, forward_kwargs: dict = {}):
'''Gets information about every layer in the graph
Args:
... |
3c33b212a28cdcff1b3f1ab4aa9f59247bf17e6ba66bdc506056f2bf8930ad95 | Python | 3,648 | 109 | #!/usr/bin/python
# -*- encoding: utf-8 -*-
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.model_zoo as modelzoo
# from modules.bn import InPlaceABNSync as BatchNorm2d
resnet18_url = 'https://download.pytorch.org/models/resnet18-5c106cde.pth'
def conv3x3(in_planes, out_planes... |
fd6907eb359d5b18d1e8c22ee34d3f8a926e18f6de124f858ebe6755ed756963 | Python | 3,648 | 124 | __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, Union
import re
import pandas as pd
from tmkit.util.Reader import Reader as greader
from tmkit.util.Writer import... |
851d59446c20d4c71dc5dfe0c59cbc4aa9267dfd2120b702129310b6751fe3ef | Python | 3,650 | 134 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 12 09:54:06 2020
@author: yokoyama
"""
from copy import deepcopy
from numpy.matlib import repmat
from numpy.random import randn, rand
import numpy as np
#%%
##############################################################################
def Sigm(v):
v0 = 6
vma... |
f17a336d22683f538f7cee685bf139a3bd5091be96debe30eed3fbb114e17276 | Python | 3,650 | 54 | """Final doc images from a gallery capture dir: per-sensor webp + composite grid."""
import os, sys
import numpy as np
from PIL import Image, ImageDraw, ImageFont
D, OUT = sys.argv[1], sys.argv[2]; os.makedirs(OUT, exist_ok=True)
S = os.path.join(D, "out")
FONT = ImageFont.truetype("/usr/share/fonts/truetype/dejavu/Dej... |
43201331833c10eb664a045430b61e33ba2454d74c54de415fe0f0ca3508007b | Python | 3,651 | 98 | #!/usr/bin/env python3
"""
File: combine_network_output.py
Created: 2020/05/19
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... |
68677f02f3fb7e925aa7375ab87522516689047837b5245c96d5d1fe61ce8d61 | Python | 3,653 | 92 | # 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... |
464123226ce8e9d5fd10c3b2c2b84bb3b9522e75b66c0587b0d0e782bd1bf178 | Python | 3,654 | 132 | import argparse
import warnings
from tqdm import tqdm
import pandas as pd
import torch
import sys
from moses.models_storage import ModelsStorage
warnings.filterwarnings("ignore", category=UserWarning)
def get_collate_fn(model):
def create_tensors(string, device):
regression_values = string[2:]
... |
e52a31e9ea27b5613ea1d0928d35063947ef45cd110427274089d9c89d8a52ab | Python | 3,655 | 102 | from mmcv.cnn import build_conv_layer, build_norm_layer
from torch import nn as nn
class ResLayer(nn.Sequential):
"""ResLayer to build ResNet style backbone.
Args:
block (nn.Module): block used to build ResLayer.
inplanes (int): inplanes of block.
planes (int): planes of block.
... |
1d87af9b640de74735873c72d39de60ac6c433b89e0a5836ae35315edbb7c068 | Python | 3,656 | 71 | import unittest
from pathlib import Path
from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
from oaklib.implementations.sparql.sparql_implementation import SparqlImplementation
from oaklib.implementations.sqldb.sql_implementation import SqlImplementation
from oaklib.resource import On... |
5a8389511ed3eac13c9669f33927b9d689b897637c2c878d8106d08d2141c870 | Python | 3,659 | 122 | import os
from skimage import io, transform
import torch
import torchvision
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import Dataset, DataLoader
from torchvision import transforms#, utils
# import torch.optim as optim
import numpy as np
from PIL imp... |
fb6186d660023812f28034f0c33b1314b40210d14a33887b284eafabdfe4da4c | Python | 3,661 | 126 | import torch
from torch.nn import Parameter
import torch.nn.functional as F
import torch.nn as nn
from torch_scatter import scatter_add, scatter_mean
from torch_geometric.utils import remove_self_loops, add_self_loops, softmax
from torch_geometric.nn.inits import uniform
from torch_geometric.nn import max_pool_x
fro... |
c515732300b4f4ba3f27cba91761049011e3b1ed5007b6e74884525d853833cc | Python | 3,662 | 79 | import functions_basic_sak as funsak
import pandas as pd
import os
import inspect
import AIS_interp
import AIS_neighbors
import AIS_parameters
import AIS_trajectory
import AIS_geopandas_tagging
import AIS_numpy_tagging
import AIS_loitering
import AIS_description
import re
import numpy as np
import datetim... |
444cdf07bbc5c3227496b0aaecb2da21fe9002a2f906fe5f7599f2331c0bacb5 | Python | 3,663 | 98 | #!/usr/bin/env python3
"""
File: combine_network_output.py
Created: 2020/05/19
Last Changed: 2022/02/10
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 F... |
d4b1e9a115fc4196dfd904e2ecfab304a4311ee79549170afef2ec905970fc74 | Python | 3,663 | 114 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pickle
import imageio
import numpy as np
import matplotlib.pyplot as plt
from PIL import Image
Image.MAX_IMAGE_PIXELS = 100000000000
'''
Fast Plotter for Large Images - Resamples Images to a target re... |
822e5b000f33ae68852a096b94274079e72298a962da627f9eb4c94be53f81b4 | Python | 3,664 | 99 | """Capture rain transitions and late sensor creation on a running CARLA server.
Example: python test_rain_runtime.py --port 4654 --town Town03_Opt --load
This changes weather and spectator pose; --load also replaces the world.
Inspect the saved images for falling streaks and lens droplets. API assertions
check state a... |
78d49aee4bbe38c3db8710504ed84a4bafaf8e2d0a528b45736b2d40e6d6b319 | Python | 3,665 | 122 |
import os
import numpy as np
import matplotlib.pyplot as plt
def calc_dfc(y, half_window):
nreg, nt = y.shape
fc = np.zeros((nt, nreg, nreg))
for i in range(half_window, nt-half_window):
fc[i] = np.corrcoef(y[:,i-half_window:i+half_window])
inds = np.triu_indices(nreg, k=1)
fc = fc[:, ... |
7a17543a04dd874b770dfb5a5b785074fc23c23749e8ae712429839a84f06547 | Python | 3,665 | 103 | from typing import Tuple
import torch
from .correct_answer import _is_correct_output
def sort_elemnts_by_another(base: any, for_sort: any):
return torch.as_tensor([x for _, x in sorted(zip(base, for_sort))])
class SubgroupFinder:
def __init__(self, dt: float = 1e-3) -> None:
self._dt = dt
... |
cb4996acdcd582ff146785b3405e27e7762c42aed3daf1a2f65165f63e216ca5 | Python | 3,666 | 93 | import mne
import numpy as np
import matplotlib.pyplot as plt
import sys
import datetime
import os
import fnmatch
import pandas as pd
import fnmatch
from mne.channels import find_ch_connectivity
from scipy import stats
from mne.stats import spatio_temporal_cluster_1samp_test
from mne.viz import plot_topomap... |
26616cc5dfddf8208e7c221fdf285fe121c3a2a9b0dd3798665a53649c10c9f7 | Python | 3,667 | 114 | # 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... |
a30f8f0db32af4dbab93f148293138ab9dbe69f0753a3a311b17743687f701f9 | Python | 3,667 | 145 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Dict
import pandas as pd
from pandas import DataFrame
from tmkit.db.cath.Reader import Reader as cathreader
def summar... |
b85d3a20f29e1344a2e779a1ec5bd1a3466dcedd1f54e9ef7ac50cbfeb9ea772 | Python | 3,668 | 102 | import torch
import networkx as nx
import numpy as np
import matplotlib.pyplot as plt
from torch_geometric.nn import GCNConv, GINConv, BatchNorm
from graphxai.datasets.BA_shapes.ba_houses import BAHouses
from sklearn.metrics import f1_score, accuracy_score, precision_score, recall_score
from graphxai.gnn_models.node_... |
3483698e09aeda552eab0f86853e8d3a69a9509fb40776020e719e92590f8579 | Python | 3,669 | 94 | # 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... |
80a62b0e0cbf70c4ac11e9db3e276c27e7794469044131655568ccd571da1306 | Python | 3,669 | 84 | """Hybrid-render patch for nre-ga serve-grpc (prototype).
Loaded through PYTHONPATH by the engine's compiled entry point. When ``nre.grpc.serve`` is
imported, ``SensorSimService.render_rgb`` gains a second behaviour: a request whose
``image_quality`` equals the sentinel ``-7`` is rendered with the engine's internal
``... |
7f872f74406692a997c5a02751ea82a8d89fe333646a68b1c012de648dda5969 | Python | 3,670 | 111 | import torch
import torch.nn as nn
from neuralop.models import FNO
class OTNO(FNO):
"""
Optimal Transport Neural Operator
The architecture is described in [1]_.
OTNO integrates optimal transport (OT) into operator learning for partial
differential equations (PDEs) on complex geometries.
Pa... |
49c8b8c86a8aaa15d2d39bf0284dea7360b8b178337c5f937d954829df1d1d00 | Python | 3,671 | 104 | # 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... |
e32b5419ad287430f3e23e29b69e296ca13415edbe0b21611192aa6a95c2db76 | Python | 3,676 | 101 | """An in-memory sqlite index for simple associations."""
import logging
import sqlite3
from collections import defaultdict
from dataclasses import dataclass, field
from typing import Any, Dict, Iterable, Iterator, List, Tuple
from semsql.sqla.semsql import TermAssociation
from sqlalchemy import Column, String, create... |
0d719f6048c2393b328d4d0d135efe97a6908c31d10d97e602febe5e8004fc1b | Python | 3,677 | 102 | import os
import math
import glob
import argparse
parser = argparse.ArgumentParser(description='Create slurm jobs to call genotype on a genomicDB')
parser.add_argument('genomicDB_dir', help='Directory that contains the merged gVCFs')
parser.add_argument('jobs_dir', help='directory to write jobs to')
parser.add_argum... |
151b2beefcb5793a986bfe6c011485ca5c21ccbd96cc3873aeb57f2508d3aed1 | Python | 3,677 | 89 | import os
import argparse
import random
import warnings
import math
from shutil import copyfile, move
from tqdm import tqdm
import concurrent.futures
import numpy as np
def copy_file_fnc(s_d):
s, d = s_d
file_name = os.path.split(s)[-1]
copyfile(s, os.path.join(d, file_name))
return int(os.path.exist... |
9da3ee39df6cf6217598caec18ccf0261d137b25716f8c39539709e9cb70f7bb | Python | 3,678 | 62 | """Walker skeleton projected on an RGB camera that follows it."""
import os, re, sys, queue, math
import numpy as np, carla
from PIL import Image, ImageDraw
sys.path.insert(0, os.path.dirname(__file__)); import scene
OUT = sys.argv[1]; os.makedirs(OUT, exist_ok=True)
ROOT = os.environ.get("CARLA_ROOT", os.path.join(os.... |
16a8ca42dcaa97d2440ac801c34167d6af003c70a3135efd6079895593176b97 | Python | 3,679 | 88 | # 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... |
703efc64bc420d0fd389f74328728b483e10544285b0bb6d5460000e9b1a4d34 | Python | 3,681 | 112 | import os, random
import torch
import numpy as np
import torch.nn.functional as F
#from tqdm import trange
import matplotlib.pyplot as plt
from torch_geometric.utils import sort_edge_index, to_undirected
from graphxai.datasets import ShapeGGen
from graphxai.datasets.load_synthetic import load_ShapeGGen
def if_edge_ex... |
fb72a8bc2703008ca2e410cbadd86cc7c4e627bf5c1bb8ba7436d2ab542df249 | Python | 3,682 | 86 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 25 11:12:36 2021
@author: paulmueller
Run for each patient a calc script but bunch up the calculation be a set of datafiles to keep runs short
"""
import os
import subprocess
import numpy as np
import glob
def write_submit_file(cmd, time_in_sec, j... |
545fb4076d94231e68fef466c767dff705124b0a4577cd2a597d922d598d7295 | Python | 3,683 | 97 | import os
import itertools
import numpy as np
import torch
from torch import nn
from .utilities import ReaderWriter
class RNNHyperparamConfig:
def __init__(self,
embed_dim,
z_dim,
num_hidden_layers,
bidirection,
p_dropout, ... |
f1cef8af67004d8df7139c90786fb49b46acb80c086023fafd4e7fde72eff58f | Python | 3,683 | 85 | import networkx as nx
import numpy as np
from scipy.interpolate import RegularGridInterpolator, LinearNDInterpolator
def graph_to_ndarray(graph):
out_nodes = np.empty((1, 3))
out_edges = np.empty((1, 3))
visited_nodes = list()
visited_node_pairs = list()
for (start_node, end_node) in graph.edges()... |
061e744bbcded569996b8269c62fedf633701c70a36daafe3ce7cb6806a064d1 | Python | 3,687 | 139 | import torch
import torch.nn as nn
import numpy as np
class Flatten(torch.nn.Module):
def forward(self, x):
batch_size = x.shape[0]
return x.view(batch_size, -1)
class unFlatten2(torch.nn.Module):
def forward(self, x):
batch_size = x.shape[0]
return x.view(batch_size, 1, 28, 2... |
c4303c73766743630abcd5cabed5d91a75a91b16a46a9341456f4428da23490d | Python | 3,689 | 129 | """Static analysis of Nottingham movie data.
"""
print("Setting up")
import os
import numpy as np
from osl_dynamics.analysis import static
from osl_dynamics.data import Data
from osl_dynamics.utils import plotting
from osl_dynamics.analysis import power, connectivity
#%% Setup
run = 1
#subjects_dir = '/well/woolri... |
369bfa9f0bc89419e336843f49ced9efe9909e10ee45c00d48b518dce0c823eb | Python | 3,691 | 100 | """Bounded native assembly probes, launched by test_callvar_assembly.py."""
from pathlib import Path
import sys
from MACS3.IO.PeakIO import PeakIO
from MACS3.Signal import RACollection as module
from MACS3.Signal.ReadAlignment import ReadAlignment
def reference(n=400):
x = 20261003
seq = bytearray()
for... |
8b541186086dc961c38a24380674e13728338d6bb8591d91b7881c443c20b6ea | Python | 3,692 | 102 | # Copyright 2021 DeepMind Technologies Limited
#
# 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 agr... |
cd2e8ac46799c7fa9649f4ae17c24e18fc77047c80d20cad27cb40d4ea11e998 | Python | 3,692 | 81 | import os
import shutil
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--dataset', type=str, required=True)
parser.add_argument('--folds', type=int, default=1, required=False)
args = parser.parse_args()
original_imgs = f"./data/{args.dataset}/images"
groundTruth_imgs = f"./data/{args.dataset}... |
b0af9dd8292bc9b89462cf95273e3513ffedd8babaee693f1337a831f04d1d3f | Python | 3,693 | 127 | #!/usr/bin/env python3
"""Tests for utils."""
from unittest.mock import patch
import numpy as np
import pytest
from phys2cvr import utils
# ## Unit tests
@pytest.mark.parametrize(
'var, dtype, out',
[
(10, 'int', 10),
(10.0, 'int', 10),
('10', 'int', 10),
([10], 'int', 10),... |
edc65c3f5cb42216a263dd484362ecc95f1eedcd95b8c5af7824914f7ea1df55 | Python | 3,694 | 79 | # Copyright 2023 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
f6b8cd02d4717e8f4e1dc6fb98d89eeca624e1c9b60621e93f8398a0a7ff335e | Python | 3,696 | 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 agreed to... |
81b7a055ece15d8216db114fe954a28ab641c3c0afea9648a1988ed3ebedc9f6 | Python | 3,697 | 114 | # 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... |
be3379819a58bd15e3c90409b9760388ecbae49c51a84e25555375eaf79e24f0 | Python | 3,697 | 102 | """
This file gets each voxel's corresponding searchlight voxel indices and outputs a matrix of num_voxels * searchlight_size
Example run:
python searchlight_get_indices.py -s 1 -m mask_path.npy -o output_path.npy
-s : subject
-m : cortical mask
-c : path to table of coco proportions organized by images x coco label... |
41633f342ed0a0d39861f1e9e389d4b89fb7faa63b1d4999dc52e56a3f7aee70 | Python | 3,698 | 85 | """Phase 3 tests: novel-odor probing pin-downs.
The headline claim of the project is that the AIF agent produces a max-entropy
DAN response on truly novel KC patterns while RPE has no such mechanism. These
tests pin down that signature on the real larval connectome.
"""
import numpy as np
from mb_dual_dan.connectome... |
5feb1e07b02b2d2d83bcab44813b4629de5662f5150a64caed00d647716984fd | Python | 3,699 | 120 | from pathlib import Path
import pytest
from conftest import RESOURCES
from ppqm import chembridge, gaussian, tasks
from ppqm.utils import shell
if shell.which(gaussian.G16_CMD) is None:
pytest.skip("Skipped. Could not find Gaussian executable", allow_module_level=True)
TEST_ENERGIES = [
("O", -51.7615037201... |
9ab0bc00dbc1fa4039fe522be332def985ee063a14c7d75f96e75114650de101 | Python | 3,699 | 125 | import threading
import numpy as np
import pytest
import torch
from backend import jobs
from backend import tracking_matcher
def descriptors(count, offset=0):
values = torch.arange(
offset,
offset + count * 4,
dtype=torch.float32,
).reshape(count, 1, 2, 2)
return values / max(flo... |
deed5e49f666e80c567a12eae52c704a63bdcc7c46ace3a57fa95d77bd3d164d | Python | 3,699 | 120 | import unittest
from linkml_runtime.linkml_model import EnumDefinition, SchemaDefinition
from linkml_runtime.loaders import yaml_loader
from oaklib.datamodels.value_set_configuration import ValueSetConfiguration
from oaklib.utilities.subsets.value_set_expander import ValueSetExpander
from tests import (
BACTERIA,... |
73af9f3aedcf7dee762a962c388bd2ceb914d5a023a1f118c9c6407278909ce8 | Python | 3,703 | 110 | import math
import torch
import torch.nn as 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', ['masked_im2col_forward', 'masked_col2im_forward'])
class ... |
a578c83162d1b4f3a55358fab913ee5266e7dac8e4c31385309d98eed6d056e8 | Python | 3,703 | 118 | import os.path
from PIL import Image as PIL_Image
import math
from subprocess import call
from charpragcap.utils.image_and_text_utils import vectorize_caption,valid_item,index_to_char,char_to_index,edit_region,get_img_from_id
from charpragcap.utils.config import *
print("rep_size",rep_size)
if __name__ == "__main__":... |
fe22f12cd416c4e1bdecb6a36d8b56b117ed270df24d3ae6a26e50e46bc708cf | Python | 3,706 | 116 | # %%
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 prom... |
6cb098623c7791eb2cfee392d65edaad0061ac6dcc6bd868fe161e3e9ab320be | Python | 3,707 | 136 | #%% [markdown]
## gzipping a connectome
# > A (perhaps silly) experiment running gzip on a connectome edgelist
#
# - toc: false
# - badges: false
# - categories: [pedigo, graspologic]
# - hide: false
# - search_exclude: false
#%%
import gzip
# edgelist_loc = "maggot_models/data/processed/2020-09-23/G.edgelist"
edgelis... |
9dc3c6ae8137ad411953e246f890a9f7fa2a66cf43385e28de4733702bcbb9e4 | Python | 3,708 | 110 | #!/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>.
import argparse
import sys
import carla
TRAFFIC_LIGHT_STATES = {
'Gree... |
af54e76cd01a80a46f9196f27bb1fd3fa8d6837a8c82bea0426db662d2c20ef2 | Python | 3,708 | 128 | import torch
import wandb
import sys
from neuralop.training import setup, AdamW
from neuralop import get_model
from neuralop.utils import get_wandb_api_key
from neuralop.losses.data_losses import LpLoss
from neuralop.training.trainer import Trainer
from neuralop.data.datasets import CarOTDataset, load_saved_ot, CFDData... |
d23a8892a26baaaac7885bff91c032230e5bf49a1f333d92a858fd00b559e57c | Python | 3,708 | 116 | #Authors: Ceyao Zhang, Renjie Li, May 2022, CUHKSZ
import numpy as np
from gym.spaces import Box, Discrete
import torch
import torch.nn as nn
from torch.distributions.normal import Normal
from torch.distributions.categorical import Categorical
def mlp(sizes, activation=nn.ReLU, output_activation=nn.Identity):
la... |
304b2839631325e5e59d1f9d40b6f0f926991c4dbc5dc5666edd3652be0deaab | Python | 3,709 | 108 | """
File: combine_eqtlprobes.py
Created: 2020/10/08
Last Changed: 2020/10/13
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... |
1ddc821045d3718007a02dd288efef9b40e69ac49cfa5ecc739edb89af1db27e | Python | 3,710 | 81 | # Parse TargetALS samplesheet to make molgenis-compute samplesheet
import os.path
import argparse
parser = argparse.ArgumentParser(description='Make Molgenis Compute samplesheet for TargetALS.')
parser.add_argument('samplesheet', help='TargetALS samplesheet')
parser.add_argument('cram_dir', help='path to cram file dir... |
7b2da7f53c1e25de3a64b409ea3548baaf7b1a1c99f9c8440cd72aafb61e5de2 | Python | 3,710 | 99 |
import matlab
import numpy as np
import sys
import AIRLOCALIZE_N5
import n5_metadata_utils as n5mu
def as_matlab(arr):
try:
np2matlabDict = {
'float64': matlab.double,
'float32': matlab.single,
'uint8': matlab.uint8,
'int8': matlab.int8,
'uint16... |
e149b8daa006d88996a8ff1db7479397a61376931925853a4ea6f4004ba16706 | Python | 3,711 | 145 | # %% [markdown]
# #
import os
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.stats import rankdata
from sklearn.decomposition import PCA
from graspy.plot import heatmap, pairplot
from graspy... |
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