sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
25d07f519b274cdfcb38ff9632fc0f62328837b8a193e0ef8b74f5d57a86c6e4 | Python | 15,042 | 335 | # Feature testing models
import torch
import numpy as np
from torch.nn import functional as F
from .resnet import *
class DeepAccNet_no3D(torch.nn.Module):
# Parameter initialization
def __init__(self,
onebody_size = 70,
twobody_size = 33,
protein_size ... |
69daf4c6bf35d57b5f8d5a0a6be24ecc1b409b1996e865a7921d486a6070b26b | Python | 15,050 | 320 | """Ground-truth preview maths. No CARLA, no clip on disk: a synthetic rig and a handful of points."""
import numpy as np
import pytest
from carla_cosmos.preview import (
BOX_EDGES,
LAYERS,
Box,
FThetaCamera,
Horizon,
PreviewCamera,
SceneGT,
box_corners,
box_edge_points,
camera... |
0e47fc7ccc7eee194feb162b84b3c87c109ca3a41b823b347bd18cb1fff34c62 | Python | 15,057 | 367 | # 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... |
59bbc728f4ee7e7cf3f99a97763882e2d7076036cd68513c53367174a285c396 | Python | 15,057 | 384 | import functools
import logging
import math
import unittest
from urllib.error import HTTPError, URLError
from oaklib.datamodels.search import SearchConfiguration
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.implementations import UbergraphImplementation
from tests import (
CELL,
CELLULAR_... |
21a671e662dd6ead3a8343bab5341b466b1b6b473f601d490fd1f660df068b02 | Python | 15,064 | 357 | from __future__ import print_function
from __future__ import absolute_import
__author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that... |
e2f655d5ccecaea1c9e273a438dfee64c18787ee2eb27fbc73128c4014b796e9 | Python | 15,065 | 424 | from __future__ import annotations
import logging
from typing import Dict, List, Type, Union
import os
import pandas as pd
import pandas as pd
import dask.array as da
import yaml
from ..data_structure.acquisition import Acquisition
from ..data_structure.experiment import Experiment
from .steps import *
class ImagePi... |
1b64ae46a9bf6a99179dad59a7942b13b730066fbba62fb07d463a0ce6402e55 | Python | 15,067 | 351 | #!/usr/bin/env python
# Copyright 2013-2019 Lukas Burget, Mireia Diez (burget@fit.vutbr.cz, mireia@fit.vutbr.cz)
#
# 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/lic... |
e6d9cbbac944835fe28c9ae2e7e93c5aa90063924eb87e65525440ebae9cc6e3 | Python | 15,071 | 326 | import torch
import torch.nn as nn
from .basic_model import BasicModel
from . import networks
from . import losses
from torch.nn import functional as F
from sklearn import metrics
class VaeMultitaskGNModel(BasicModel):
"""
This class implements the VAE multitasking model with GradNorm, using the VAE framework... |
7fffd82cc2fa0fcbf2290cbffc78468960ac82e988d1c53cb399ab52f5a46833 | Python | 15,090 | 363 | """
File: main.py
Created: 2020/03/19
Last Changed: 2020/03/20
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 ... |
306b30bcae0e85f2db0a36327d0c83042f047ceec05756d34afcdd8773b6486a | Python | 15,095 | 359 | # 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... |
3b19d9dde9438138ab376a2f4b707852dfb122712148d76357c67480e502cfd8 | Python | 15,104 | 373 | # 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... |
7c1e10fa6974400dd4d35bfd2e4704f51ad4c8ca334b4e4b577f082606ec9497 | Python | 15,114 | 487 | # 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... |
82abab2328348a4f44322d0a3a5f4110a93a731c2b619be677e52cda2acba085 | Python | 15,127 | 451 | __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, Optional, Union
import subprocess
from tmkit.interface.Tool import Tool
class MSA(Tool):
"""
This class ... |
e2a9d0d6d0ca935f050069281f2ce8aeb9aa2d08468210a09c82c26e033633cf | Python | 15,136 | 429 | import nibabel as nib
import logging
import numpy as np
import os
import os.path as op
from time import time
import pandas as pd
import pimms
from dipy.align import resample
from AFQ.tasks.utils import get_fname, with_name, str_to_desc
import AFQ.utils.volume as auv
from AFQ.viz.utils import Viz
import AFQ.utils.str... |
c42de01769fa068d4d82635998a5dae9ee28e804951f4a66b7026595c4753f19 | Python | 15,138 | 550 | # %% [markdown]
# #
import itertools
import os
import time
from itertools import chain
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 anytree import LevelOrderGroupIter, Node, RenderTree
from joblib ... |
fc085c4de119285800555abd60c7e071dcb023782aae90f014e0473de16a2359 | Python | 15,147 | 587 | # %% [markdown]
# ## Imports
import os
import time
from itertools import chain
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 src.data import load_metagraph
from src.graph import preprocess
from src.io import sav... |
8a4ac465cdcdbdbaa0d7b363f8770817fcd5038a20d74740657aa4d03d1bb978 | Python | 15,159 | 484 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""
Variant of the resnet module that takes cfg as an argument.
Example usage. Strings may be specified in the config file.
model = ResNet(
"StemWithFixedBatchNorm",
"BottleneckWithFixedBatchNorm",
"ResNet50StagesTo4",
... |
5affa3d48457acf50be981e96198abae909ffdb9e54dc51531641b14ea4d2eff | Python | 15,165 | 548 | # %% [markdown]
# ##
import os
import warnings
from itertools import chain
import matplotlib as mpl
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns
from joblib import Parallel, delayed
from sc... |
f3dc46c3b67f81d598f482b35eec06f1e70c474316315018e9b68a6cbba2e5cb | Python | 15,169 | 374 | import sys
import os.path
import itertools
from PySide2 import QtCore, QtGui
from PySide2.QtWidgets import QApplication, QMainWindow, QGridLayout, QWidget, QPushButton, QLayout, QDialog, QLabel, QRadioButton, QVBoxLayout, QFileDialog
import numpy as np
import pyqtgraph as pg
import pandas as pd
def sanitizeList(l):
... |
08a31905bc89b7626f09139011ad6dd34ed44b030ab69f7ee5aeaeee72f68922 | Python | 15,195 | 381 | import numpy as np
import pandas as pd
from pathlib import Path
from utils.metrics import IoU
from utils.sets import difference, intersection, union
def evaluate_object_detection(df_detections, df_annotated_slices, print_confusion_matrix=False, print_scans=False):
# Loop over predictions
print('Found p... |
65ba1c3a445d408ad2d1bc3eb307364a99d5bea6e74274e10803a226808d4882 | Python | 15,213 | 555 | # %% [markdown]
# ##
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import matplotlib as mpl
import numpy as np
import pandas as pd
import seaborn as sns
from src.data import load_metagraph
from src.hierarchy import signal_flow
from src.visualization import adjplot, CLASS_COLOR_DICT
from src... |
524af7a24eaf221e31adc17fd03ad63c3092d7ea2836929d06b3d15f921a524b | Python | 15,224 | 455 | #!/usr/bin/python
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
... |
cf9548f50a2e3d50aeb47ef23d3f9230b54734adf0793ff4be818fa024164ddb | Python | 15,234 | 424 | from __future__ import annotations
import json
import logging
from glob import glob
import secrets
from subprocess import call
import pandas as pd
import os
import json
import matplotlib.pyplot as plt
from typing import List
import numpy as np
from typing import TYPE_CHECKING
from .acquisition import Acquisition
cla... |
36f81f420b0e295ad1936150720167253fdfabdeca6a1c236c95fdd986deab00 | Python | 15,253 | 442 | import numpy as np
import scipy.signal
import matplotlib.pyplot as plt
import matplotlib
plt.switch_backend('agg')
import sys
import pandas as pd
import os
import pickle
from multiprocessing import Pool
from itertools import repeat
import utils.EventDetection_utils as EventDetection_utils
import utils.general_util... |
24dd2707f13cc6215c2d9fc78a8127f3ca0f4877996abcde6a499c4fe7937575 | Python | 15,264 | 439 | # 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... |
dc1293c8676ceae03cc5128024317983b671bed594ed5d24c450514008e14d66 | Python | 15,265 | 436 | import toml
import datetime
import platform
import os.path as op
from argparse import ArgumentParser
from funcargparse import FuncArgParser
from AFQ.definitions.image import * # interprets masks loaded from toml
from AFQ.definitions.mapping import * # interprets mappings loaded from toml
from AFQ.api.bundle_dict im... |
cacf1afefadc8b5b710fb87fe05088e3d51b2a2e32dcddb4e6ea3ef76913a0bc | Python | 15,271 | 561 | #%% Imports and file loading
import glob
import json
import pprint
import sys
from operator import itemgetter
from os import listdir
from pathlib import Path
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
from graspy.plot import gridplot
from src.data import load_networkx
from src.pymaid i... |
606e0627afdc0f909d3ecb23b28f9cfcb2abe2661071578cbcfc983330085a6a | Python | 15,275 | 392 | import argparse
import builtins
import math
import os
import random
import shutil
import time
import warnings
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.distributed as dist
import torch.optim
import torch.multiprocessing as mp
import torch.utils.data
i... |
6be4fc3aa79ce2f2beee2acde6df708283bccb74c41dcc9b8233b7ca4e079e61 | Python | 15,275 | 456 | # Copyright (c) Open-MMLab. All rights reserved.
import numbers
import cv2
import numpy as np
from .io import imread_backend
try:
from PIL import Image
except ImportError:
Image = None
def _scale_size(size, scale):
"""Rescale a size by a ratio.
Args:
size (tuple[int]): (w, h).
scal... |
cb193866df4b83b899fcaac54b013295bbf3a240350e3fee8d31b104c8d25b7f | Python | 15,277 | 502 | # %% [markdown]
# ##
import os
import time
import colorcet as cc
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.linalg import orthogonal_procrustes
from tqdm import tqdm
from graspy.cluster import GaussianCluster
from graspy.embed import AdjacencySpectralEmbed
... |
2f43850ec3c3b9ddd1116923cc20b05dbd015e4c83428b9f13e67e08706be2e6 | Python | 15,289 | 414 | # Copyright (c) Open-MMLab. All rights reserved.
import logging
import os.path as osp
import warnings
from abc import ABCMeta, abstractmethod
import torch
from torch.optim import Optimizer
import mmcv
from ..parallel import is_module_wrapper
from .checkpoint import load_checkpoint
from .dist_utils import get_dist_inf... |
1b21f76e8e4dfa933102dc6ebcbe43eeed09fc7b5251fe19fdf55ec0ea4bd8b2 | Python | 15,292 | 415 | # Copyright (c) Open-MMLab. All rights reserved.
from math import cos, pi
from .hook import HOOKS, Hook
class LrUpdaterHook(Hook):
"""LR Scheduler in MMCV.
Args:
by_epoch (bool): LR changes epoch by epoch
warmup (string): Type of warmup used. It can be None(use no warmup),
'const... |
f958e697acc1fbd84754f941d21527613868c7f893f3b5e5e3e654a5a6c9bd84 | Python | 15,299 | 452 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import time
import os
import torch
from tqdm import tqdm
import numpy as np
from maskrcnn_benchmark.config import cfg
from maskrcnn_benchmark.data.datasets.evaluation import evaluate
from ..utils.comm import is_main_process, get_wo... |
d1968c7b80823631ec288ae48f267fe9074c27e7852460c5595a6b882c20276b | Python | 15,310 | 383 | """
To update previous RACCOON clustering runs with new data.
F. Comitani @2021-2022
"""
import os
import sys
import pickle
import logging
DEBUG_R = 15
import time
import psutil
import random
import warnings
warnings.filterwarnings("ignore", category=FutureWarning)
from raccoon.clustering import IterativeClus... |
beba070e517faa7f19bfe16778922c2dd3467fecdb04d9a9cea63ec15aec2767 | Python | 15,316 | 420 | import nibabel as nib
import numpy as np
from time import time
import logging
import pimms
import multiprocessing
from AFQ.tasks.decorators import as_file, as_img
from AFQ.tasks.utils import with_name
from AFQ.definitions.utils import Definition
import AFQ.tractography.tractography as aft
from AFQ.tasks.utils import ... |
4860e7883b95a26d1af877286426fda3f1539c13c38122ba26058e431a7c0f50 | Python | 15,319 | 387 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
920af8c3e44e0af2dc63dde94242eae75228c795295bdeff7b3828888399f568 | Python | 15,326 | 425 | # coding=utf-8
# Copyright 2020 The Google Research Authors.
#
# 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 applicab... |
1b15fa3799bb682d66eac48dd0f6f7ab6e1469549228937c3a1e6482802a2e16 | Python | 15,331 | 407 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.model_zoo as model_zoo
class DeepLabV3Plus(nn.Module):
def __init__(self, classes=2, aux=True, os=16, pretrained=False, _print=False):
if _print:
print("Constructing DeepLabv3+ model...")
... |
e26d80da95bed42e169d3fcbefed354d4ec2fa8dbdf888c20d8397d02dc6e209 | Python | 15,339 | 377 | # 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... |
83085bfc3cb08d21b38124abaf0d833b73f3290fa4c57ac597762ec75b1d5c3d | Python | 15,355 | 522 | # %% [markdown]
# ##
import os
import warnings
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns
from joblib import Parallel, delayed
from scipy.stats import poisson
from sklearn.exceptions import Convergence... |
4875002ab1a15b26998c566b6d6dfdf04a436907d7beb4f247cf35432d6c6607 | Python | 15,362 | 290 | #!/usr/bin/env python3.9
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 1 14:51:53 2021
@author: paulmueller
Calculates autocorrelation/crosscorrelation functions for a patient and writes them out for sws,aed,roi combinations.
OUTFORMAT for each ROI (TOTAL,MT,LIP,LPFC,OFC,ACC)
total,SWS,nonSWS,low_AED,high_AED,SWS_l... |
8303c9be755898be8e4239aa244570554de2d22a2c828e0af5e25df7e9b407bb | Python | 15,384 | 334 | import torch
from ..builder import BBOX_ASSIGNERS
from ..iou_calculators import build_iou_calculator
from .assign_result import AssignResult
from .base_assigner import BaseAssigner
def scale_boxes(bboxes, scale):
"""Expand an array of boxes by a given scale.
Args:
bboxes (Tensor): Shape (m, 4)
... |
9ff25003553e06c17eb02030cab54c8007a1e4cb66bf02cb776541ff7f3d2618 | Python | 15,386 | 449 | '''
@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 argparse
import logging
import os
import sys
import numpy as np
import pandas as pd
import torch
from torch.utils.data import WeightedRandomSampler, DataLoader, T... |
122f9da53a368dcbc1c80b13d351676d4a2481fe95ce6fddc9f85a365c9b9cc1 | Python | 15,391 | 417 | """
Code for estimating retinotopic parameters with AFNIs circular population
receptive field mapping and neuropythy to further refine these estimates and
delineate retinotopic regions.
Requires a preprocessed version of the dataset stored in bidsdata/derivatives/fmriprep. Further non-python dependencies: FSL, AFNI
U... |
ef59da0326433c412378c32b5810053488b34d7116c03021626ba524a4e999c3 | Python | 15,394 | 376 | import logging, os
from transformers.modeling_outputs import SequenceClassifierOutput
from transformers.models.roberta.modeling_roberta import RobertaModel, RobertaPreTrainedModel, RobertaClassificationHead
from torch.nn import MSELoss, CrossEntropyLoss
from torch import mean, stack
number_inputs = 8
class MultiInpu... |
ba57c2e094e8b559a27e7dfeceaaa3373f129399c359a10862703e4b84f8c699 | Python | 15,405 | 376 | import logging, os
from transformers.modeling_outputs import SequenceClassifierOutput
from transformers.models.roberta.modeling_roberta import RobertaModel, RobertaPreTrainedModel, RobertaClassificationHead
from torch.nn import MSELoss, CrossEntropyLoss
from torch import mean, stack
number_inputs = 8
class MultiInpu... |
d5c0e733d8eac54ed3e123e2a752ad88079ce70eb9d601818b341284b21791fb | Python | 15,406 | 442 | #!/usr/bin/env python3
"""
Statistical module for phys2cvr.
Attributes
----------
LGR :
Logger
"""
import logging
import os
import numpy as np
from numpy.lib.stride_tricks import sliding_window_view as swv
from scipy.stats import zscore
R2MODEL = ['full', 'partial', 'intercept', 'adj_full', 'adj_partial', 'adj_... |
a74edaf2b2d7ed28f63f225b2fc2f7a5d21b87c213cfa2b0d164f2ee980773ad | Python | 15,407 | 321 | import torch
import torch.nn as nn
def get_dist_and_masks(embeddings, labels):
n = embeddings.size(0)
# L2 distance:
dist = torch.norm(embeddings[:, None] - embeddings, dim=2, p=2)
mask_pos = labels.expand(n, n).eq(labels.expand(n, n).t())
mask_neg = ~mask_pos
mask_pos[torch.eye(n).bool()] =... |
6cd364379e04a9b9e4d47eeb8af1b6ba61b674fbdfef8883e1a52de853bdaa11 | Python | 15,411 | 413 | from __future__ import print_function, division
import csv
import functools
import json
#import you
import random
import warnings
import math
import numpy as np
import torch
import os
from pymatgen.core.structure import Structure
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader i... |
61317bafb13bb5f9954d72ec68e330088a695fb1407297c52e30dd9695e03d9d | Python | 15,420 | 419 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from math import floor, log10
from os import makedirs
from os.path import basename, dirname, exists, expanduser, isdir, join
import matplotlib as mpl
import numpy as np
from . import fmtxt, plot, testnd
from .plot._base import POINT
from ._data_obj import combi... |
d5f0315b6558625d644e3b490f22ec368abbcecccb20dece8dc2ad66d6ebe4e2 | Python | 15,425 | 372 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This library is free ... |
503fc940075e73e4af687ecc03b6ac814589084788c5b5985dd674ceec290594 | Python | 15,444 | 567 | #%% Imports and file loading
import glob
import json
import pprint
import sys
from operator import itemgetter
from os import listdir
from pathlib import Path
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
from graspy.plot import gridplot
from src.data import load_networkx
from src.pymaid i... |
b9fab4f3582931359c246dc6d6faf5ad4dac6854317b67f18d4d7162495a8f23 | Python | 15,460 | 207 | """Reference-led wheel detail pass. Keeps the original Blender source untouched.
Geometry is an artist reconstruction, not Michelin manufacturing CAD.
Run with Blender --background --python <this file>.
"""
import bpy,bmesh,math,json,os
import numpy as np
from pathlib import Path
from mathutils import Vector,Matrix,Qua... |
2bf90581f82fd07b4f052970d99903586ff53f4b02b56bd82cc277cb68f4bd84 | Python | 15,466 | 508 | import argparse
import math
import random
import os
import numpy as np
import torch
from torch import nn, autograd, optim
from torch.nn import functional as F
from torch.utils import data
import torch.distributed as dist
from torchvision import transforms, utils
from tqdm import tqdm
from dataset impo... |
609b32daafd4eb2de2af17f859380f5fa250d4684301bb2649c3583bdaeee74f | Python | 15,469 | 406 | """
Copyright (c) 2019, National Institute of Informatics
All rights reserved.
Author: Huy H. Nguyen
-----------------------------------------------------
Script for fine-tuning ClassNSeg (the proposed method)
"""
import os
import random
import torch
import torch.backends.cudnn as cudnn
import numpy as np
... |
ec3e5a9a7622c7c69889f11dec280aa1a369a88d835f5e89fc88356006466d58 | Python | 15,471 | 328 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'
import tensorflow.keras.layers as kl
import tensorflow as tf
from tensorflo... |
bbc19eab7917255714ca13d381a86299e1d6fd02e72edf7340755cb7d1f0e925 | Python | 15,480 | 478 | import itk
import numpy as np
import pandas as pd
from monai.transforms.transform import MapTransform, Transform
import json
from pathlib import Path
# these are my custom monai style transforms
class SaveITKImaged(object):
def __init__(self, keys, output_filename=None, out_dir=None, output_postfix=None):
... |
048b1629b186eab974a05a58bc83a180705e68d31e2fd6bc7dabda744a4b18a4 | Python | 15,490 | 299 | # Author Romain Sala
import numpy as np
import scipy
import scipy.stats
from statsmodels import robust
from tqdm import tqdm
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from statsmodels.stats.multitest import multipletests
class RobustGaussianSurprise:
""" Method to dectect bursts and pa... |
19b97ea872ad2cae287ed9db85ad4ffb10c6b24eff68b354f781fd7038c915ce | Python | 15,510 | 328 | import argparse
import sys
import collections
from pathlib import Path
import csv
import os
import pandas as pd
import numpy as np
import torch
import torch.nn.functional as F
from tqdm import tqdm
import data_loader.data_loaders as module_data
import model.loss as module_loss
import model.metric as module_metric
fr... |
6d3b9fc3857d8982056104312ac07733cf12e64ce8f35b0b175540ccb0b61f70 | Python | 15,515 | 444 | import time
from typing import Tuple
import torch
import pickle
import pathlib
import numpy as np
import statsmodels.api as sm
from scipy.stats import zscore
from hebbcl.trainer import Optimiser
from copy import deepcopy
from utils.nnet import from_gpu
from utils.eval import (
compute_accuracy,
compute_relchan... |
7045cac22f2375ce663499f54b3949a38598f8b66f7ba5f1933953b3214d392c | Python | 15,533 | 385 | import logging
from collections import defaultdict
from collections.abc import Iterator
from copy import deepcopy
from typing import Dict, Iterable, List, Optional, Tuple
import networkx as nx
from sssom import Mapping
from oaklib.datamodels.cross_ontology_diff import (
DiffCategory,
MappingCardinalityEnum,
... |
7ceefb461f439cd4659a229356a3915a324ac2c4fc1d3d9dc0c25b5be2c8ea8a | Python | 15,546 | 375 | import os
import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from lmfit import Model
import helper_functions as hfn
import plotting_functions as plotfn
from scipy import stats
from lmfit.models import PowerLawModel
from lmfit.models import LinearModel
def expfunc(x, a, b):
return a... |
a587dd8454ecb4fa3b89896ec2885b4b36e193e95e0eaf2fab6e836584ad8c2a | Python | 15,551 | 335 | import numpy as np
from .coupling import CouplingNode, PhaseStyle
from .forward import ForwardMesh
from ..typing import Callable, List, Optional, Tuple
from ..utils import random_vector
def _tree(indices: np.ndarray, n_rails: int, start: int = 0, column: int = 0,
balanced: bool = True) -> List[CouplingNode... |
e3e80ca6742c2a2520e4f0d8f82fdcc1c8b457358077d409ae84f3b89d05df73 | Python | 15,553 | 404 | import torch
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import add_self_loops, degree, softmax
from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool, GlobalAttention, Set2Set
import torch.nn.functional as F
from torch_scatter import scatter_add
from torch_geomet... |
b714a8806fe22f510aa06247942c2f9f526927fcf5e7a11de60ba9bd4e65b277 | Python | 15,569 | 400 | import sys
from skimage import io
import os, os.path
import math
import h5py
import time
import numpy as np
import pandas as pd
import pickle
import more_itertools as mit
import matplotlib.pyplot as plt
plt.switch_backend('agg')
import pandas as pd
import utils.general_utils as general_utils
import utils.plot_utils a... |
f2a29cf36715e1d403796fab8e909843437214472bad5f8cdfba7993225256ae | Python | 15,574 | 444 | import logging
from collections import defaultdict
from copy import copy
from dataclasses import dataclass
from enum import Enum
from pathlib import Path
from typing import Dict, Iterator, List, Optional, TextIO, Tuple, Union
import click
import sssom_schema as sssom
import yaml
from linkml_renderer.style.model import... |
a34281aa4a77f59f030390fe9a674ecd62f022e7b917b2b6dea24f1a3c143504 | Python | 15,576 | 359 | #!/bin/bash
# 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 ... |
af8c57d8770fbef916b6919c6073d394b2a04832e915ff9fe289705bd568d637 | Python | 15,577 | 358 | """
MODULE VERSION:
Module that handles production simulations and energy calculation LJ+coul CHOL_Prot/(CHOL_Prot+POPC_Prot)
"""
import os
import core.settings as CoreSettings
import core.system as System
import core.gromacs as Gromacs
import core.gromacs_commands
import user.usersettings as UserSettings
... |
5d2dc5d33235c08fbe5556b013529eb0d086bfe7963023e90e11ae14f9aee8c8 | Python | 15,585 | 321 |
import os
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.ticker as plticker
from PIL import Image, ImageEnhance
from scipy import ndimage
import warnings
warnings.simplefilter('ignore', Image.DecompressionBombWarning)
def preprocess_histology(histology_folder):
"""
Purpose
---------... |
3822659695ea6324dea578e26b0f01cd89c001763dc46c505501e2fcab07c1de | Python | 15,588 | 519 | import pickle
import numpy as np
from joblib import Parallel, delayed
from scipy.optimize import curve_fit
from scipy.io import loadmat
from utils.eval import gen_behav_models
from typing import List
from scipy.optimize import minimize
def softmax(x: np.array, T=1e-3) -> np.array:
"""softmax non-linearity
Ar... |
7e85a2b25c91198a0fef772cc9f077b5e5492eb3e4e11e9f5659ac1c6f343161 | Python | 15,594 | 407 | # 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... |
c17e243ffdae9cd4ca71c46608bd8f561ae41f23845a0b7780db8b5850992ebe | Python | 15,594 | 466 | """
Copyright 2020 - by Jerome Tubiana (jertubiana@gmail.com)
All rights reserved
Permission is granted for anyone to copy, use, or modify this
software for any uncommercial purposes, provided this copyright
notice is retained, and note is made of any changes that have
been made. This softwar... |
6522bba1e6e936de30b5f5edd9be49c7e4b4581f19bfb05ac4130a2d6c6062bf | Python | 15,598 | 360 | """FastAPI application factory.
Routes (all under ``/v1`` need ``Authorization: Bearer <token>`` except health):
===================================== ==========================================================
``GET /v1/health/live`` process is up
``GET /v1/health/ready`` 200 when every ... |
c2d16a3644c4b9aebf1b19410ac6c2bc45fbd53ae8a462f0f6190da2f46d07ad | Python | 15,603 | 381 | # -*- coding: utf-8 -*-
"""Provides a set of semi-automatically generated interfaces for all the QUIT fitting commands.
These all have to go in one file so pickling works correctly
"""
import json
from copy import deepcopy
from os import path, getcwd
from nipype import logging
from nipype.utils.filemanip import fn... |
afe9574e23ef72057391c47aebd4a58602c46a74592019143735a1c39bfaa8a8 | Python | 15,606 | 397 | #!/usr/bin/env python3
"""
File: visualise_decon_eqtl.py
Created: 2021/12/20
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 Free... |
57c56b99d09a34d199f7fb9fbd3afb10b976719b8f67b165693e6367d01821fa | Python | 15,611 | 405 | import math
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from ..utils import kaiming_init
from .registry import PLUGIN_LAYERS
@PLUGIN_LAYERS.register_module()
class GeneralizedAttention(nn.Module):
"""GeneralizedAttention module.
See 'An Empirical Study of Spatial A... |
9d58f4618f3765309b0e532f4db98d55291e82fa3fe72a44b17d6786965d8d27 | Python | 15,619 | 319 | import operator
from copy import deepcopy
from distutils.version import StrictVersion
from typing import Dict, Optional
import allennlp
import numpy as np
import torch
import torch.nn.functional as F
from allennlp.common import Params
from allennlp.data import Instance
from allennlp.data import Vocabulary
from allennl... |
3c0489d7965bde753ca046a0e0ca24327aa5011a676279aad88b5aea265b40b5 | Python | 15,621 | 484 | from typing import List, Optional, Union
import torch
from torch import nn
from torch_harmonics import RealSHT, InverseRealSHT
import tensorly as tl
from tensorly.plugins import use_opt_einsum
from tltorch.factorized_tensors.core import FactorizedTensor
from neuralop.utils import validate_scaling_factor
from .base_s... |
894345c75c01952da4b4d02279ac54d27e7362b31b8c259a08b734b6eea1cec0 | Python | 15,656 | 388 | from cmath import log
import os
import csv
import yaml
import shutil
import sys
import time
import warnings
import numpy as np
import pandas as pd
from random import sample
from sklearn import metrics
from datetime import datetime
import argparse
from model.utils import *
import torch
import torch.nn as nn
import torc... |
0aa17f88a16b22ef62ce0a6910f2633c88ad3f58a42dbf52f56182b0a529d5df | Python | 15,658 | 377 | # 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... |
16b400d2bc5bd10063eefce69ab0b5ac54a5c7bcad416bf50cbf9270f903b2d2 | Python | 15,685 | 376 | # Copyright 2020-2021 The Kubeflow Authors
#
# 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 ... |
04674bedbfefef8cebf1d8e5d7616af79b560632c195fcb5b7b698b5e9866326 | Python | 15,686 | 311 | """
Script for training a model on a set of data
Should be called form within a U-Time project directory, call 'ut init' first.
All hyperparameters should be stored in the hparams.yaml file (generated by
ut init).
"""
import logging
import numpy as np
import os
import tables
import tensorflow as tf
from argparse impor... |
4d0ac6d71bf5d461c1e5a3cff09dd59189a46f6f59443c3f44509466ceca6483 | Python | 15,687 | 528 | #!/usr/bin/env python
import sys, os
import unetsl.data
import numpy
import skimage.morphology
import skimage.draw
import skimage.measure
from skimage.feature import peak_local_max
from skimage.morphology import watershed
import scipy.ndimage.filters as filters
from scipy.ndimage.morphology import distance_transfo... |
c1b10f4551d81671e46803d48917cc4fa67efa47d1d5f5991993b08490c445c8 | Python | 15,688 | 489 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Implementation of nipype interfaces for QUIT MT module
Requires that the QUIT tools are in your your system path
"""
from os import path
from copy import deepcopy
from nipype.interfaces.base import TraitedSpec, DynamicTraitedSpec, File, traits, isdefined
from qipype.... |
f5e47ffcd61d6fe82d9fea2bace8e5992824137a8f72bda3849ec70ae6bb562a | Python | 15,697 | 414 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
85be1571fd9cf38cd0db9d7b87068a721d3ddcfae680a1e486bc88cb1bd2d5f6 | Python | 15,710 | 361 | """
File: inter_eqtl_effect.py
Created: 2020/03/16
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 Foundation, eithe... |
d147916fc30a74c68c9403b42f89d6682c07353909f432baaba51f4b9be3f361 | Python | 15,712 | 380 | import numpy as np
import os
import sys
import time
import torch
import torch.nn.functional as F
from torchvision import transforms
from torch.optim.lr_scheduler import ReduceLROnPlateau
import torch.nn.init as init
from model.dense_ed import DenseED
import random
import pandas as pd
#import matplotlib.pyplot as plt
im... |
40e5beb63d5a11f2d7a7056293bc4a16242617b184122a012ea47f62a7e25f95 | Python | 15,722 | 404 | ####################################################################################################
# Copyright (c) 2019, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free softwar... |
7a3321860dd1709dd82dff8a69ced404b7a0d162501473332336e9ef891290f3 | Python | 15,723 | 406 | import logging
import unittest
from copy import deepcopy
from kgcl_schema.datamodel import kgcl
from oaklib.datamodels import obograph
from oaklib.datamodels.search import SearchConfiguration
from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
from oaklib.datamodels.vocabulary import HAS_P... |
62977557cb95f1375bf39edf396eafb54cffe0aca5687e6024239b219321edb7 | Python | 15,733 | 570 | # %% [markdown]
# #
import itertools
import os
import time
from itertools import chain
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 anytree import LevelOrderGroupIter, Node, RenderTree
from joblib ... |
6b1023b3dbfc1aeb0c980ec70cb97e620376341fe40f0b3f91291d49eefe2831 | Python | 15,740 | 471 | import os.path
import pickle
import sys
import pandas as pd
import numpy as np
from tqdm import tqdm
import behavelet
import utils2p
import utils2p.synchronization
import flydf
root_dir=os.path.abspath("../..")+'/'
# print(root_dir)
# root_dir="/mnt/data/CLC/"
annotation_dir=root_dir+"Ascending_neuron_screen_analy... |
8e2362097e7494fe5f7397388a5e201348339f7adf06572715042c245d0b1b70 | Python | 15,743 | 363 | #!/usr/bin/env python3
"""
File: sn_simple_eqtl_plot.py
Created: 2020/11/27
Last Changed: 2020/12/02
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... |
7d344958a3140d3c2bc9dedbf6e5fdcd1bde277e896c998c495ac1272fa7fcfa | Python | 15,755 | 392 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from copy import deepcopy
from .._exceptions import DefinitionError
from .._text import enumeration
from .definitions import Definition, typed_arg
def assemble_epochs(epoch_def, epoch_default):
epochs = {}
secondary_epochs = {}
super_epochs = {}
... |
9ae1f75649bb43b27b3e8aaba81f286e5233f367e9e3b85061045a2c864324a5 | Python | 15,766 | 404 | """
File: inter_eqtl_effect_celltype.py
Created: 2020/04/20
Last Changed: 2020/06/16
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 Foundati... |
b487717efb8cf3e2d08cebd7fbcc035aef5a33dff176ab2d9a3d203d2a34f6f6 | Python | 15,767 | 387 | #!/usr/bin/env python
# Process a cigar string.
# Note that this module includes a set of unit tests, which can be
# executed by running this file directly from the command line.
import os
import sys
import re # for regular expressions
import math
from tt_log import logger
VERSION = '20150707.... |
1a89478f781e5e8b9041ca7d948452913e91dcf1eaca978d993c94b34cee9465 | Python | 15,776 | 503 | # Auto generated from item_list.yaml by pythongen.py version: 0.9.0
# Generation date: 2023-04-13T19:34:47
# Schema: itemList
#
# id: https://w3id.org/oak/item-list
# description: A data model for representing simple lists of entities such as genes. The data model is based on
# the schema.org ItemList clas... |
ba7ee397096f0e9766fd449759bf36282f70bc51fe2b0361aa9afa08a9ff8ef6 | Python | 15,780 | 347 | import os, sys
# currentdir = os.path.dirname(os.path.realpath(__file__))
# parentdir = os.path.dirname(currentdir)
# sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
#
# PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'
import tensorflow.keras.layers as kl
import tensorflow.keras.backe... |
9f31de2de9e843e1fc1d452f9197502ea414e84b90a4fc2a8e6a89c1ff67f742 | Python | 15,783 | 414 | """
tests
Created by: Martin Sicho
On: 31.05.22, 10:20
"""
import os.path
import tempfile
from collections import OrderedDict
from unittest import TestCase
import pandas as pd
from drugex.data.corpus.corpus import SequenceCorpus
from drugex.data.corpus.vocabulary import VocSmiles, VocGraph, VocGPT
from drugex.data.f... |
533f071b52672d3217bc6af9c5fd44977ac82eef71a495e26393686141208f32 | Python | 15,810 | 448 | # adapted from https://github.com/molecularsets/moses/blob/7b8f83b21a9b7ded493349ec8ef292384ce2bb52/moses/metrics/metrics.py
import torch
import warnings
from multiprocessing import Pool
import numpy as np
from scipy.spatial.distance import cosine as cos_distance
from scipy.stats import wasserstein_distance
# scikit-... |
3c70eb5a132aa6d31df5f8ee875ef56d5b01c32edb87199b7fc4b7adbc9f9197 | Python | 15,814 | 383 | import os
import pkgconfig
import sys
from copy import deepcopy
from platform import system, uname
from psutil import cpu_count
from subprocess import check_call
from pybind11.setup_helpers import Pybind11Extension, build_ext, WIN, MACOS
from setuptools import find_packages, setup
# Loop through command line arguments... |
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