sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2dba12194684271def5f0531a55aa6803d0670a6d6c5fd27ef19883dec195c36 | Python | 5,225 | 131 | # 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 math
import random
import time
import carla
from . import SmokeTest
# The packaged build o... |
e8d04d3f1fb6bdbe443073b33822ba5436620a1edd8c8680cbec04a2bed7d36b | Python | 5,227 | 151 | #%%
import sys
sys.path.append("/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/")
import pymaid
import pyoctree
from pymaid_creds import url, name, password, token
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
rm = pymaid.CatmaidInstance(url, token, name, pas... |
1cea44cf2888f948ed6b8d9f380e87e06c42d604668813daa549967a6172aa7c | Python | 5,228 | 159 | # Copyright (c) Open-MMLab. All rights reserved.
import os
import os.path as osp
import subprocess
import tempfile
from mmcv.utils import requires_executable
@requires_executable('ffmpeg')
def convert_video(in_file,
out_file,
print_cmd=False,
pre_options='',
... |
9aab3ae2ac3e3416245f25f42c4a17136c64be6dd24e276bea6641b65964d53a | Python | 5,228 | 154 | #!/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
"""
... |
e89225091862e31fdef18d1c5f46539936ca2b9e6786b542e8ca7b35d837ee7f | Python | 5,228 | 137 | """Test building of the MP table."""
from logging import Logger
from typing import List
from unittest import mock
from unittest.mock import MagicMock
import pandas as pd
import pytest
from pytest_mock.plugin import MockerFixture # type: ignore
from fi_parliament_tools import mptable
@pytest.fixture
def mp_data() -... |
5fa9cce59028b5a5370a02bc81fb44b955e6006697cfcce438173ecbf62175de | Python | 5,231 | 185 | #!/usr/bin/env python
# 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 copy
import numpy as np
import torch
from optrepo import OptRepo
def compute_federated_algorithm(weights_list, model, args,... |
9bcc635ca4befd5d22f2a56a379e41bb966c234f45c4aff81b5323d84a5ba0ab | Python | 5,236 | 226 | # Using Skorch
import torch
import skorch
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from torch import optim
from torch.utils.data import DataLoader
# Basic Functions we use in Skorch
from skorch import NeuralNet
from skorch.callbacks import EpochTimer
from skorch.callbacks import PrintLog... |
95ce99ecde34dc2b9d77a373cff70dd3a12fd4f68803aa79fe23efd25f77f87d | Python | 5,239 | 111 | # basic imports
import numpy as np
# framework imports
from cobel.memory_modules.sfma_memory import SFMAMemory
class SFMAMemoryNonLocal(SFMAMemory):
def __init__(self, interface_OAI, number_of_actions: int, gamma: float = 0.99, decay_inhibition: float = 0.9, decay_strength: float = 1., learning_rate: f... |
eb2aabf23331188c441afda5b88f00112f97902e9181c4a82f665cb422bb2902 | Python | 5,239 | 163 | import math
import torch
import torch.nn.functional as F
from torch import nn
from torch.nn import Parameter
from .config import device, num_classes
class SEBlock(nn.Module):
def __init__(self, channel, reduction=16):
super(SEBlock, self).__init__()
self.avg_pool = nn.AdaptiveAvgPool2d(1)
... |
8811ec2a391982fe30edfa7993be8ca6ceaf28292b9dbe4b47a6ff8ba1a2ac67 | Python | 5,246 | 137 | #!/usr/bin/env python3
"""List and toggle a map's environment objects (buildings, vegetation, poles...).
Commands:
labels list valid CityObjectLabel names
list [--label Buildings] [--name PATTERN] count/sample matching objects
disable --label Buildings [--name P] [... |
544f6f78cf3f5d83ff779445821d18c9772051ab0c191fcfcd9a0efb7d0b331c | Python | 5,249 | 126 | import numpy as np
import os
import json
import argparse
'''
Script for converting unlabeled videos from CalMS21 .json files into .npz files for input into TREBA.
The .npz files are stacked trajectories of length N (default = 21).
In our work, we use the unlabeled videos set (first 229 videos for train
and the remai... |
58942de05202f0fbe491c312e6da9520b449f7f7e2aed4910a775116e6430293 | Python | 5,250 | 167 | """Hyperbolic layers."""
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init as init
from torch.nn.modules.module import Module
from layers.att_layers import DenseAtt
def get_dim_act_curv(args):
"""
Helper function to get dimension and activation at every laye... |
787c8340bd4b35020e9934dbc52e6f02b8b1c2c3fcd87aef0cf5c22cf2f357a9 | Python | 5,251 | 118 | ##########################################################
## ccAF: classifyPrimaryCells_homoSapiens.py ##
## ______ ______ __ __ ##
## /\ __ \ /\ ___\ /\ \/\ \ ##
## \ \ __ \ \ \___ \ \ \ \_\ \ ##
## \ \_\ \_\ \/\_____\ ... |
f8db34c1f018d13304f67153ffac7ea88106e5f67854602b7e54fbb95bf0fd99 | Python | 5,251 | 72 | """Live check of sensor.camera.rt_lens with camera_model=ftheta (NuRec / NVIDIA rig pixel-distance -> angle polynomial):
spawns a small prop at known positions, finds its image centroid, and compares with the analytic projection
theta = sum c_i r^i solved for r. Also checks exposure_mode=manual gives a non-black, dete... |
1e638d0af41df88a5e952efac9586abac83de3d2d089dea30cb484089ecf48d0 | Python | 5,254 | 130 | #%%
from pymaid_creds import url, name, password, token
from data_settings import pairs_path, data_date
import pymaid
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
import networkx as nx
from contools import Promat, Prograph
# allows text to be editable in Illustrator
pl... |
fe9b485061d2ed3251d8645ce9b78700bf66640031b2b87e871b57a71f37ebfb | Python | 5,254 | 122 | import math
import numpy as np
import pandas as pd
from scipy import interpolate
def interpolate_predictions(segment_probabilities: np.array, segment_times: list, sfreq: float, influence=0.5):
"""Returns CNN predictions interpolated for each sample of the EEG signal.
Args:
segment_probabilities (nu... |
29032dc1e8be0e474461eea690bc8d300f19ea46fb82ff9851b0647779ed6210 | Python | 5,255 | 154 | """
This script adds manually recorded temperature values to single trial data from original data for F1311
There are two ways to achieve this:
- Start from scratch (i.e. go through all data)
- Label only those trials that were previously manually selected (i.e. where only cooled trials were included in the data, whic... |
92800f571159cdb6ecc05850b210b751454c57102cc7ae378d7d3365926f93b7 | Python | 5,255 | 196 | import fnmatch
import numpy as np
import pandas as pd
from tqdm.auto import tqdm
#from rl_analysis.util import star
from toolz.itertoolz import concat
from itertools import repeat, count
#from rl_analysis.util import syll_onset, syll_duration
# mice with bad fiber placement
EXCLUDE_MICE = (
'186',
'189',
'... |
b9957de347c8b84d64962bf672cbd72dacbad0f48a40c4b1ee2feff07e3f3446 | Python | 5,255 | 131 | #!/usr/bin/env python3
# Copyright 2020 Johns Hopkins University (Author: Desh Raj)
# Apache 2.0
# This script is based on the Bayesian HMM-based xvector clustering
# code released by BUTSpeech at: https://github.com/BUTSpeechFIT/VBx.
# Note that this assumes that the provided labels are for a single
# recording. So t... |
57f59c9279c5007ffad25e8a5bf99fbe773c19f583a2949bb53be3438c79345d | Python | 5,257 | 130 | # 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... |
77cb095d01754dc1a971f06196692cb08b95a3ebbf94a781b64dad0a868314f7 | Python | 5,258 | 147 | # 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... |
d95df9751e240a2162f30235e75ea1bc7ed7433ab827cd4961326855aa9a3fb9 | Python | 5,259 | 163 | #!/usr/bin/env bash
# =============================================================================
# Copyright 2019 Pavel Yakubovskiy, Sasha Illarionov. 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 ob... |
7eef51ed66888d3c4255854e82de75b266df967de8e7d51504168bacc0ca5d46 | Python | 5,260 | 143 | # 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... |
c1a5f6d904580624a4379496a3783b1a7fa59e54541b207b09e4de267943eb9b | Python | 5,265 | 167 | # Validate NML, createLEMS, simulate, create chart js, and validate js of a model
# Usage:
# To generate voltage clamp plots:
#
# createModelVCplots.py path/to/channel.nml Na/Kv/Cav/Kca/Ih [dtInMs]
#
# NOTE: this script assumes and has only been tested on linux OS (Ubuntu 16)
# WHY??? Because the devs of the tools u... |
cb79631d9436b11d81427b61f1dc8812a7846cf783ffab15d8beab1c09043b0a | Python | 5,267 | 97 | from functions import *
import pickle
import matplotlib.pyplot as plt
GiacoPath = "./28nets_rules/Giacomantonio2010.txt"
starttime = datetime.now()
#Running this script required 0.6sec on a MacBook Pro with a 2.3GHz Quad-Core processor and 16 GB of RAM
#Plot Figure 4 comparing the results of a single state transitio... |
31a361b8d0dc32b3e63712e501bc647ed57b73a0e015c441c7008276c313c6e9 | Python | 5,268 | 112 | import numpy as np
from scipy.interpolate import CubicSpline
import warnings
warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
def scaling(dataset, sigma=0.1):
factor = np.random.normal(loc=1., scale=sigma, size=(
dataset.shape[0], dataset.shape[2]))
data_scaled = np.multiply(dat... |
42013cd4bce564ef795df42fdd57206bdd346746f85804e63eaf7ad5c2ad473c | Python | 5,273 | 150 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 17:03:58
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 19:19:47
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... |
22f6a8515ad038568f7b1dd1006d207d253bd52f06dff06c4352fe674154421e | Python | 5,274 | 138 | '''
Use `trianle library` to create mesh.
'''
import numpy as np
def triangulate_with_triangle(points, max_area, add_code=''):
'''
Create triangulation using *triangle* library (don't forget to cite it)
Parameters: q - quality meshing (restrict triangles angles to be smaller than 20 degrees),
... |
7681392b749c6a6a417174e4d519ce7cbb48df813cfe53eff6d9303badcbefaa | Python | 5,274 | 179 | import torch
from PIL import Image
extensions = ['.jpg', '.jpeg', '.png', '.ppm', '.bmp', '.pgm', '.tif']
def pil_loader(path):
# open path as file to avoid ResourceWarning (https://github.com/python-pillow/Pillow/issues/835)
with open(path, 'rb') as f:
img = Image.open(f)
return img.conver... |
073d340823b982ecb5ab2ea86d27298f7bf7e9c9307338cd47cdfc799caa0e97 | Python | 5,275 | 199 | import argparse
def get_parser(parser=None):
if parser is None:
parser = argparse.ArgumentParser()
# Model
model_arg = parser.add_argument_group("Model")
model_arg.add_argument(
"--q_cell",
type=str,
default="gru",
choices=["gru"],
help="Encoder rnn cel... |
461c9d3dcb1693b4d91f368ad1048005f868e252f9e5ab45f6ee00fa7e5bcb2e | Python | 5,275 | 129 | #!/usr/bin/env python3
"""What blueprints may a generated scenario name?
Two different answers, and a scenario is only safe where they agree:
build inventory what the CARLA build can actually spawn. Read from
$CARLA_ROOT/.../Content/Carla/Config/*Parameters.json - the
defin... |
716b6124859055c6ca67f1528ffffd64092cb2e950f539232e6d8266103a612b | Python | 5,277 | 167 | from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import spearmanr
from .Tools import raiseExpectedGot
class FrequencyInputCurve(object):
"""A frequency vs. input curve fitted to data."""
summary_metrics = [
'f',
'I',
'CV',
'rheoba... |
ccc2b1af83d343f04980915f7e18e3844cb2a868203223047074edbff3a7276f | Python | 5,278 | 106 | #!/usr/bin/env python3
# -*- coding: utf-8 -*
"""Gait study analysis file.
"""
import os
import glob
import pandas as pd
import numpy as np
from scipy.signal import savgol_filter
from sklearn.linear_model import LinearRegression
from sklearn.metrics import r2_score, mean_squared_error, mean_absolute_error
def main... |
2fc7466e4106a67448f7a50d3e3dd795812da98e79f312934a8d2a3f65a05fd7 | Python | 5,279 | 149 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from torch import nn
from torch.nn import functional as F
from maskrcnn_benchmark.modeling import registry
from maskrcnn_benchmark.modeling.backbone import resnet
from maskrcnn_benchmark.modeling.poolers import Pooler
from maskrcnn_be... |
a16f8af2802ba383ef0eb9ff7f61658d5b90079c99bcb2d19ba7db15a3f8226f | Python | 5,280 | 134 | import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import normal_init
from mmcv.ops import nms
from ..builder import HEADS
from .guided_anchor_head import GuidedAnchorHead
from .rpn_test_mixin import RPNTestMixin
@HEADS.register_module()
class GARPNHead(RPNTestMixin, GuidedAnchorHead):
... |
d7cdecaa47be271679ff2238b7788957cf016e06b9604f60950d355d8eb108e1 | Python | 5,280 | 103 | # basic imports
import numpy as np
import pickle
import matplotlib.pyplot as plt
def countInvalidTransitions(invalid_transitions: list, mode='default') -> dict:
'''
This function computes the fraction of invalid transitions
that were replayed in the second and third environment.
Param... |
05017043ccfb5b622330d5f6c219d0361eda48fcebd0983063466b8f9ef3f361 | Python | 5,281 | 138 | """
Copyright (c) 2019, National Institute of Informatics
All rights reserved.
Author: Huy H. Nguyen
-----------------------------------------------------
Script for making FaceForensics++ FaceSwap dataset
"""
import argparse
import cv2
import numpy as np
import os
import sys
parser = argparse.ArgumentP... |
1a6cde8d0852eba06cfe9fa8a3bdb06bc54dd847e38f13a9f913ae28d173bee7 | Python | 5,283 | 146 | from pylab import *
def plotCurrentscape(voltage, currents):
# make a copy of currents
# CURRENTSCAPE CALCULATION STARTS HERE.
curr = array(currents)
cpos = curr.copy()
cpos[curr < 0] = 0
cneg = curr.copy()
cneg[curr > 0] = 0
normapos = sum(abs(array(cpos)), axis=0)
n... |
7f10763edd5742d336e548ae8575ffd81e49903a5838451454f711eee86bb69b | Python | 5,283 | 142 | import logging
import tarfile
import tempfile
from dataclasses import dataclass, field
from typing import ClassVar, Dict, List, Optional
from urllib.parse import urlparse
from urllib.request import urlretrieve
import pystow
import requests
import requests_cache
from defusedxml.ElementTree import fromstring
from oakli... |
b1406713903ff106a159702f7ebd096096b0197e3697d8abc34989d337c3620e | Python | 5,286 | 138 | """
Copyright (c) 2019, National Institute of Informatics
All rights reserved.
Author: Huy H. Nguyen
-----------------------------------------------------
Script for making FaceForensics++ DeepFakes dataset
"""
import argparse
import cv2
import numpy as np
import os
import sys
parser = argparse.Argument... |
145b04fb6bb9005994850acc24b6f733ebf4b30970df105c36e498aae7d1a71a | Python | 5,287 | 153 | # 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... |
f13bc7642a3fef770c5c35553d51d942d0a4fd12b111657d1214f5016f31f6b5 | Python | 5,289 | 125 | import numpy as np
def get_test_patches(img, crop_size, stride_size, rl=False):
test_img = []
test_img.append(img)
test_img = np.asarray(test_img)
# test_img_adjust=img_process(test_img,rl=rl)
test_img_adjust = test_img
test_imgs = paint_border(test_img_adjust, crop_size, stride_size)
... |
7787d07acca18557e9a1850ebd6b4e55e19538665cb9976118a407509437097d | Python | 5,290 | 126 | #%%
from data_settings import data_date, pairs_path
from pymaid_creds import url, name, password, token
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
import numpy as np
import pandas as pd
import pickle
from contools import Promat, Adjacency_matrix, Celltype_Analyzer, Celltype, Cascade_Analyz... |
bc6f93444039d581fcd445a5c704a7102650fec9ee5bbde4cc40af4e0334a882 | Python | 5,290 | 128 | # %%
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
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
from contools import Celltype, Celltype_Analyzer, P... |
0ec01d1534b10fe7e2caab84e67e07211026130355bf848d8fedd797e7e36eeb | Python | 5,291 | 210 | import matplotlib as mpl
import matplotlib.pylab as plt
from matplotlib.lines import Line2D
import numpy as np
import pandas as pd
import seaborn as sns
def make_up_axis(ax):
ax.xaxis.set_ticks_position('bottom')
ax.yaxis.set_ticks_position('left')
ax.spines['left'].set_color('#333333')
ax.spines['bo... |
93b33df25b75211f184cae7ab08df840501ec8565cbe6c9936af88dbf372b112 | Python | 5,291 | 64 | """Make M_CarPaintMaster render sanely under path tracing (editor Python commandlet).
The car-paint master is a clear-coat material whose instances carry Roughness values up to 1.6 (invalid; the raster
path clamps them and fakes rough-metal reflections from reflection captures, so the cars look glossy anyway). The pat... |
a7194f70773c698734f45f906b314c4cbff96574f1f2f8f5e635358010fb90f9 | Python | 5,293 | 162 | import ipdb
import torch
import numpy as np
import scipy.stats as st
import sklearn.metrics as metrics
from tqdm import trange
from sklearn.model_selection import KFold
from sklearn.metrics import f1_score, accuracy_score, precision_score, recall_score
from graphxai.datasets.shape_graph import ShapeGGen
from graphxai.... |
a3df9bff8aa0b50df06dcec04ce823960175967422c08b22abfdc7950c7199e3 | Python | 5,294 | 135 | # 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... |
91beb877b5b95aa194fe07e4812e6f3c80e688969c5cabeed9c0348e1128a9d9 | Python | 5,296 | 183 | import numpy as np
import matplotlib.pyplot as plt
import time
from helper import *
from ALsim import ALsim
import sim
import sys
import os
from ALsimParameters import std_paras
import random
import scipy.optimize as opt
from genome import set_x
connect_I= "hom"
dirname="opt-dir"
paras= std_paras()
paras["dirname"]= d... |
d5103b354b71acb3377760887549db7426a00d2f60cf7ae2c9a6e6ab1f03a051 | Python | 5,297 | 141 | """Worker <-> server protocol: newline-delimited JSON over a unix socket.
The worker **binds** the socket; the server connects (one connection per
operation, so a ``cancel`` can arrive while a ``run`` is streaming). Every
request carries ``op`` and ``id``; every reply carries the same ``id`` and an
``event``:
======... |
f1503a844a52518d869382727aed75f0cb0a543b2ec0d6abf9bea605f3ba1de0 | Python | 5,297 | 204 | #! /usr/bin/python
# -*- coding: utf-8 -*-
import tensorflow as tf
from tensorflow.python.util.deprecation import deprecated
__all__ = [
'identity',
'ramp',
'leaky_relu',
'swish',
'sign',
'pixel_wise_softmax',
'linear',
'lrelu',
]
@deprecated("2018-06-30", "This API will be deprecate... |
2185ba036cfff5234f80241675fcc5516924a552e20688c345d9bd84b4d55bfa | Python | 5,299 | 166 | # coding=utf-8
# Copyright (c) 2021, NVIDIA CORPORATION. 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 re... |
66a1056431bffb83732453ac7c67f9bb894ec411caad1ef895ef1ed741036274 | Python | 5,306 | 146 | import torch
from mmcv.ops.nms import batched_nms
from mmdet.core.bbox.iou_calculators import bbox_overlaps
def multiclass_nms(multi_bboxes,
multi_scores,
score_thr,
nms_cfg,
max_num=-1,
score_factors=None):
"""NMS for... |
1b4d7a503d9ce7ad568d78c8ea887acac67dc54929ab945d8ca5e130c1be96f4 | Python | 5,311 | 141 | from utils.inference_dataset import InferenceDataset
import sys
sys.path.append(".")
sys.path.append("..")
from models.psp import pSp
from utils.test_options import TestOptions
from utils.common import tensor2im, log_input_image
from configs import data_configs
import os
from argparse import Namespace
from tqdm import... |
8c9048372307a217b7db9f5ccfadd47a78853aa1653018f6e6839eb2d4b5635a | Python | 5,312 | 129 | import mmcv
import torch.nn as nn
import torch.nn.functional as F
from ..builder import LOSSES
from .utils import weight_reduce_loss
@mmcv.jit(derivate=True, coderize=True)
def varifocal_loss(pred,
target,
weight=None,
alpha=0.75,
gamma=2.0,... |
05a3992c42f7c56d847360334d8fc902c16b484a68fda4a5b50f6275845b4cc8 | Python | 5,316 | 143 | import random
import numpy as np
import torch
from mmcv.parallel import MMDataParallel, MMDistributedDataParallel
from mmcv.runner import (HOOKS, DistSamplerSeedHook, EpochBasedRunner,
Fp16OptimizerHook, OptimizerHook, build_optimizer)
from mmcv.utils import build_from_cfg
from mmdet.core imp... |
72b26cf0aa4c87b8be27c8f221e0091c9d94dd23e2063dd727d774d7bcabad0f | Python | 5,316 | 143 | import random
import numpy as np
import torch
from mmcv.parallel import MMDataParallel, MMDistributedDataParallel
from mmcv.runner import (HOOKS, DistSamplerSeedHook, EpochBasedRunner,
OptimizerHook, build_optimizer)
from mmcv.utils import build_from_cfg
from mmdet.core import DistEvalHook, E... |
fbf787953015a91936e2c82d5ba81445d5b7c2d86022d22d20f904989ac4e125 | Python | 5,318 | 143 | import jax
import jax.numpy as jnp
import numpyro
import numpyro.distributions as dist
import numpy as np
from jax import random
# regression model with continuous-valued outputs/responses
# http://num.pyro.ai/en/stable/examples/horseshoe_regression.html
def horseshoe_regression(X, Y, indicator=None):
D_X = X.sha... |
2ef0df73e5dfc5f6defbbd482158da6788de2f4af7a350577ecb72dc58ec689d | Python | 5,324 | 200 | #%%
import os
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
import pymaid
from graspologic.embed import AdjacencySpectralEmbed
from graspologic.utils import binarize, pass_to_ranks, remove_loops
from src.data import load_metagraph
from src.graph imp... |
430a208cbb495ef32972e45b4b958578ca96a6edc61196382ad86b5d6455bad5 | Python | 5,324 | 179 | """
custom gym environment developed for invoking FDTD simulations used in DQN.
Author: Renjie Li. October 2021 @ NOEL.
"""
from src import FdtdRl
import random
import gym
from gym import spaces, logger
from gym import utils
from gym.utils import seeding
from collections import namedtuple, deque
from itert... |
8be43eb9b05148981dd688df5b3cf2e48450f8aca77bc1dabd7d3d126301cce0 | Python | 5,324 | 159 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-15 19:42:42
LastEditors: Naiyuan liu
LastEditTime: 2021-11-15 20:01:47
Description:
'''
import cv2
import numpy as np
from skimage import transform as trans
src1 = np.array([[51.642, 50.115], [57.617, 49.990], [35.740, 69.007],
... |
6e3cb362b93dcceba8a1db24679ec24155716629cbf69ac73c9091f0ea5cb42d | Python | 5,325 | 125 | """Paper Figure 2: RPE acquisition + extinction on the larval MB connectome.
Layout (1 x 3):
A — Acquisition curve with N=20 seed variance bands
B — DAN prediction error decay across acquisition + extinction
C — Extinction kinetics showing signed-weight requirement
The claim this figure supports: signed-weight ... |
aecf23c238d38044d1550c3c9249560f3153340c1b20c9904bc11efed88b0218 | Python | 5,325 | 206 | #%%
import datetime
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.ticker import ScalarFormatter
from pkg.io import FIG_PATH, OUT_PATH, get_environment_variables
from pkg.io import glue as default_glue
from pkg.io import savefig
from pkg.plot im... |
0eb6956852d83a353445b6419a592435faff4fa1b7943da598dc83095e7383b4 | Python | 5,330 | 169 | import serial
import threading
import time
import matplotlib.pyplot as plt
from matplotlib import gridspec
# please specify the port name
PORT_NAME = "COM4"
# Parameters for serial communication
# If you change these parameters, you must also change the vhdl code on the FPGA
BAUD_RATE = 1000000 # baud rate
NUM_DATA =... |
36eef287b377b295e1eb13956262e7da37caa3da50e98263031b011f29e7b266 | Python | 5,336 | 132 | ############Test
import os
import argparse
import tensorflow as tf
from keras.backend import tensorflow_backend
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
config = tf.ConfigProto(gpu_options=tf.GPUOptions(allow_growth=True))
session = tf.Session(config=config)
tensorflow_backend.set_session(session)
from utils import... |
72efd4b78ac121a3422180b8d21a7e31a18937686b4d67f42378796e71a784e8 | Python | 5,340 | 126 | import time
import cv2
import torch
import numpy as np
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torchvision.transforms.functional as TF
from loguru import logger
from tqdm import tqdm
from trainer import Trainer
from utils.helpers import dir_exists, remove_files, double_threshold_iteration
from... |
6151e2cb9d6b73462fc538f73cb34a7c7d26f2018b0d37eb1c239224ab544cd7 | Python | 5,341 | 161 | from datetime import datetime
from pathlib import Path
from tqdm.auto import tqdm
import wandb
import torch
from torch import nn
from torch.nn import L1Loss
from transformers import ViTPreTrainedModel, ViTModel, AdamW, get_scheduler
from transformers.modeling_outputs import SequenceClassifierOutput
class ViTForRegr... |
f7935721524638981ef94fa105d5977816528349555017eb31842378989c0f71 | Python | 5,344 | 140 | import contextlib
from importlib import import_module
from AFQ.viz.utils import viz_import_msg_error
import pimms
from funcargparse import FuncArgParser
import logging
import warnings
from dipy.io.stateful_tractogram import set_sft_logger_level
with contextlib.suppress(Exception): # only works on python 3.9
fro... |
be340fd8ab121f31bc18127288ec37436d30180470058e6d223e81cdd80dd69c | Python | 5,345 | 153 | import argparse
import copy
import os
import os.path as osp
import time
import mmcv
import torch
from mmcv import Config, DictAction
from mmcv.runner import init_dist
from mmdet import __version__
from mmdet.apis import set_random_seed, train_detector
from mmdet.datasets import build_dataset
from mmdet.models import ... |
7a8a353176fc7bbad6a914597933adf47da13ef8fd5709f618ad9916b67c8bb3 | Python | 5,347 | 166 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
import os
import pandas as pd
from Bio.PDB import PDBList
from tmkit.util.Kit import batchRename, delete, ungz, urlliby, rename
from tmkit.... |
c13bc37559cfae75610092bf3bf6e6779ebd66bfc371c4955dac29d4605b2f4a | Python | 5,350 | 152 | '''
Fig. 8.
Calculation of motion vectors with asynchronous ciliary reversal.
'''
from hydrodynamics import *
import numpy as np
from pylab import *
import matplotlib.font_manager as fm
from matplotlib import gridspec
from mpl_toolkits.axes_grid1 import make_axes_locatable
import matplotlib.patches as mpatches
fontpro... |
aec579dec6444ab68ca8c82166103571baf5c6f2208dd4d4fe2bb919c5568c30 | Python | 5,351 | 165 | #### Analysis on experiments
# Built-in
import os,gc,glob,time,functools
# Libs
import numpy as np
import pandas as pd
from scipy import stats
# Plot
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import seaborn as sns
from matplotlib.backends.backend_pdf ... |
cbe7900a535d05027c996c13911cb48b856178a0281909c08bbf1586cea58705 | Python | 5,356 | 148 | from abc import abstractmethod
import torch
import torch.nn as nn
import torch.nn.functional as F
from ..cnn import ConvModule
class BaseMergeCell(nn.Module):
"""The basic class for cells used in NAS-FPN and NAS-FCOS.
BaseMergeCell takes 2 inputs. After applying concolution
on them, they are resized to... |
f008afd2173ed5654d058cffc8f5aa8eb4916b5e9c237f3fdbeba5e86d890a52 | Python | 5,357 | 152 | import pandas as pd
import logging
import numpy as np
import torch
import math, os, shutil
import functools
import matplotlib.pyplot as plt
from typing import Tuple
from torch import nn, Tensor
from torch._C import TensorType
import torch.nn.functional as F
import torch.optim as optim
from torch.optim import optimizer
... |
3e5a67966e706870b938e1b00eb56770fb6d3e0439018aa06d236f8ca863e114 | Python | 5,358 | 146 | """
========================================
Using Subject Space ROIs from Freesurfer
========================================
An example using the AFQ API to find bundles
as defined by endpoint ROIs from freesurfer.
This example can be modified to work with ROIs
in subject space from pipelines other than freesurfer.
... |
d1293c8aed38c17f0acbdbf4782bc5a82d8e6038fad7db994b739dedb026aef7 | Python | 5,362 | 130 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import numpy as np
import cv2
import os
import torch
import torchvision
from maskrcnn_benchmark.utils.comm import get_rank
from maskrcnn_benchmark.structures.bounding_box import BoxList
from maskrcnn_benchmark.structures.segmentation_mask import ... |
e4e7c26c1cb1a8a54fa02fbf1167a3aa937154f2a82c0d5b540a993c3108f517 | Python | 5,363 | 164 | __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, List, Union
import warnings
import pandas as pd
from Bio import BiopythonWarning
from tmkit.chain.PDB import PDB ... |
d85274c5e443034a5c193cb25ee4af63a428220c2f8c1f500175db5d76dcd369 | Python | 5,365 | 125 | """tan_projection.py - Estimating covariance matrix and projecting onto the tangent space
Author: Ruiqi Chen
Version: 02/08/2022
Usage: tan_projection.py <residual_dir> <rsfMRI_dir> <good_ic_file> <n_sub> <output_file>
- residual_dir: output of convert_res.sh, with one folder for each subject
- rsfMRI_dir: all resti... |
55904996df1738f58328db0c75a6619018adcd5c4460c7dc81e0b791b1cd0657 | Python | 5,367 | 142 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from torch.nn import functional as F
from maskrcnn_benchmark.layers import smooth_l1_loss
from maskrcnn_benchmark.modeling.matcher import Matcher
from maskrcnn_benchmark.structures.boxlist_ops import boxlist_iou
from maskrcnn_benchmar... |
ba067bd80caf7049a351aef9c2221b1fae08f6dc384c07cd49bec7599ec4129c | Python | 5,368 | 133 | import numpy as np
"""
Parse the command line argument to create the right initial conditions/connectivity for
the LN -> PN inhibitory connections. Options are:either
homogeneous (equal strength) signalled by correl == None or according to
correlations (corr0 without self-inhibition, corr1 with self-inhibition)
or acc... |
1201e380e84aa838f23d69c73b66abfb2da4bf695881a2a1e5b793f213deb0c0 | Python | 5,369 | 107 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'melodicompTemplate.ui'
#
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
... |
14998a2b75e75b05e19ba7f7fe2306c8fd29045f7465433a3e8a122fb650a59c | Python | 5,369 | 134 | '''
Written by Nathan Neeteson.
A set of basic utilities for importing AIM images into numpy and PyTorch formats.
'''
import vtkbone
import numpy as np
from vtk.util.numpy_support import vtk_to_numpy
import torch
from bonelab.util.aim_calibration_header import get_aim_density_equation
def get_data_and_pos_from_AIM(fn... |
55b335a5235832b101e39ff3d060a3c70b20a4af5d39b3723c71bcbf750c12d1 | Python | 5,369 | 147 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .registry import CONV_LAYERS
def conv_ws_2d(input,
weight,
bias=None,
stride=1,
padding=0,
dilation=1,
groups=1,
eps=1e-5):
c_in = weigh... |
c67663be09c504aab2cc0fc97b6236d98ca4a91f85f1b339fe138797e6549775 | Python | 5,370 | 140 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
import os
import numpy as np
import torch
from torch.autograd import Variable
from logging import getLogger
logger = getLogge... |
fe0c68f2cf3e381829139925d35e1818781773d2bf1c92e236858a64f49611e6 | Python | 5,370 | 136 | ##########################################################
## ccAF: sensitivityAnalysis.py ##
## ______ ______ __ __ ##
## /\ __ \ /\ ___\ /\ \/\ \ ##
## \ \ __ \ \ \___ \ \ \ \_\ \ ##
## \ \_\ \_\ \/\_____\ ... |
61098ba9d764cd402ca83ac25ee148e970269708c7a3f70738a95291d646f0ea | Python | 5,371 | 125 | import numpy as np
import sys
import time
import shutil
import subprocess
import os
import pyflann
from IPython.core.debugger import set_trace
from Bio.PDB import *
struct_dir = "/home/gainza/lpdi_fs/masif_paper/masif/data/masif_ppi_search/data_preparation/01-benchmark_pdbs/"
benchmark_list_fn = "../benchmark_list.txt... |
b71db42efcbeed1f19a442b468300df636da4b4f44eb1528c2a64710b9c3b0b2 | Python | 5,371 | 136 | ##########################################################
## ccAF: sensitivityAnalysis_run.py ##
## ______ ______ __ __ ##
## /\ __ \ /\ ___\ /\ \/\ \ ##
## \ \ __ \ \ \___ \ \ \ \_\ \ ##
## \ \_\ \_\ \/\_____\ ... |
2db9a6a226e8949d5e58e7fd5a946f643a58798de1b9d97e33c2c52aaab98252 | Python | 5,372 | 150 | from mip.get_nn import get_nn
from helper.misc import inference, infer_and_accuracy, clear_print, get_network_size,strip_network
from helper.data import load_data, get_architecture
from helper.fairness import equalized_odds, demographic_parity
from gd.gd_nn import GD_NN
import argparse
import numpy as np
from pdb impor... |
64a54e38192b12307778d8066b7b53c620a855549e46b7cbed8424756e658ea1 | Python | 5,373 | 158 | from dataclasses import dataclass
from typing import Dict, List, Optional
import click
import numpy as np
from oaklib import BasicOntologyInterface, get_adapter
from oaklib.datamodels.association import Association
from oaklib.interfaces.association_provider_interface import AssociationProviderInterface
from oaklib.i... |
05c7728da016d762a5e04fe4f29f9fc0f5709dd8fea97cc6368744b979f9e43b | Python | 5,376 | 139 | """
rewards
Created by: Martin Sicho
On: 26.06.22, 18:07
"""
import numpy as np
from rdkit import Chem, DataStructs
from drugex.training.interfaces import RewardScheme, RankingStrategy
from drugex.utils.fingerprints import get_fingerprint
class NSGAIIRanking(RankingStrategy):
def __call__(self, smiles, scores):... |
1b7646f1b93f3a1e96064b3e80738741b74a12f9b4db913b5d258f7cf54fd922 | Python | 5,376 | 141 | #!/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>.
"""
Deterministic collisions example for CARLA
Runs the same crash several t... |
c4065dcf10dbce22a3a3385d80ca42338189ec7ca3f6a7355e44f2d49eb42aaa | Python | 5,377 | 160 | import argparse
import glob
import os
parser = argparse.ArgumentParser(description='Generate rMATs files.')
parser.add_argument('output_directory', help='Outputdir to write results to')
parser.add_argument('jobs_directory', help='Directory to write jobs to')
parser.add_argument('cram_base_directory', help='Directory w... |
2a080333dcc01df972782af3e796a96b3067a0382d2b35c4f6952515a77c2762 | Python | 5,379 | 133 | ###################################################################
####
#### Version: 1.1.7
#### Date: 6/24/2023
#### Description: This file contains the class definition for the Time object
#### Author: Evan Cobb
####
###################################################################
import sys
import globvar as g... |
795d17ee852ca2e80438149e681fa0cb34669e1a6ed29d678947c6b99294f5c1 | Python | 5,383 | 153 | """
File: perform_deconvolution.py
Created: 2020/06/29
Last Changed: 2021/09/30
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, ... |
a28eadf2d65aa113fe053fe36c91674866159976a36e734521021c9e3fa2bbab | Python | 5,385 | 123 | import warnings
import pandas as pd
import plotly.express as px
import plotly.graph_objects as go
from constants.constants import *
from constants.enumerates import StatMeasures
from utils.helpers import list_intersection, experiment_name_format
pd.set_option('mode.chained_assignment', None)
def plot_radar_chart(dat... |
4945a8b09671256cb8129b4cec63ea2008ff02e2f8c65c6f8b462b090c5cf994 | Python | 5,387 | 186 | # model settings
input_size = 300
model = dict(
type='SingleStageDetectorSearch',
pretrained=dict(
use_load=True,
load_path='./seed_mbv2.pt',
seed_num_layers=[1, 1, 2, 3, 4, 3, 3, 1, 1] # mbv2
),
backbone=dict(
type='SSDLiteBackbone',
input_size=input_size,
... |
6649e5f44f3c57d0e4fa000ce048441a65271f2d27a5e8c21322c78ab7ce81e4 | Python | 5,390 | 113 | # Code from ResNet Architecture in DeepAccNet
# Source: https://github.com/hiranumn/DeepAccNet/blob/main/deepAccNet_noPyRosetta/resnet.py
import torch
from torch.nn import functional as F
class ResNet(torch.nn.Module):
# Parameter initialization
def __init__(self,
num_channel,
... |
f81cc0a755b84f61fbf3ac9f3c194a0f76b091421ccbf12e391d232a070b574f | Python | 5,390 | 134 | import torch
from .vae_basic_model import VaeBasicModel
from . import networks
from . import losses
class VaeSurvivalModel(VaeBasicModel):
"""
This class implements the VAE survival model, using the VAE framework with the survival prediction downstream task.
"""
@staticmethod
def modify_commandli... |
4e0f46afd1121e07e98ab53f5231b9d10e6899b0ee0f6df17145a406d25a0c64 | Python | 5,392 | 152 | """Generic case-level metadata loader for CROPro.
A metadata file maps case identifiers to clinical / label information.
Configure through the ``[metadata]`` section of a dataset schema TOML::
[metadata]
# Path to the CSV or TSV containing case-level information.
csv_path = "dataset/MyDataset/label... |
592d4c9cbb7c9f3fb73a65dde738cbc297cdba94f36ebeb316f8595d64dbc60d | Python | 5,392 | 168 | from math import sqrt
import numpy as np
import pandas as pd
from skimage import io, filters, morphology, measure, color, util, segmentation
from skimage.feature import blob_log
from skimage.draw import circle
# from skimage.external import tifffile
from scipy.ndimage import convolve
import matplotlib.pyplot as plt
i... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.