sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6c63c5fe44e0e018f1ed30c78fd8a28ca964c81888263d6b6e7d3a6de6e00305 | Python | 37,770 | 1,073 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
from __future__ import annotations
from typing import Callable, Tuple
import numpy as np
import pytest
import torch
from torch import Tensor, eye, nn, o... |
d6a93a439bf3daf43a992818c2d5e0802ba293884f558df3310f82e3f28ac8b3 | Python | 37,868 | 891 | """weights2c.py
This file is part of keras2c
Copyright 2020 Rory Conlin
Licensed under LGPLv3
https://github.com/f0uriest/keras2c
Gets weights and other parameters from each layer and writes to C file
"""
# Imports
import numpy as np
from keras2c.io_parsing import layer_type, get_layer_io_names, get_model_io_names
fr... |
24e7630f3352a91b3599449e6d2bd580a0931ac5dde8ca7ee32feb07e231ad2a | Python | 37,875 | 875 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
import os
from os import path
import scipy.stats as st
from tqdm.notebook import tqdm
from collections import defaultdict
import cv2
import imageio
import random
from eye_tracking.eye_tracking import get_eye... |
133e748afcfd6160bb9114c76c78bf882c896ff8409797cdcb9febe4ce64d55a | Python | 37,902 | 991 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import math
from typing import Optional, Tuple
import torch
import torch.nn.functional as F
from torch import nn
class PositionalEncoder(nn.Module):
... |
d66c5b4c039bf90771b1807924615aa9bd9baf9ff4506c6e483c0b73b07e5794 | Python | 37,941 | 791 | # Copyright (C) 2022-2025 ETH Zurich, Jakob Teetz and other DASH contributors.
import os
import numpy
import pickle
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from typing import Optional
from collections import defaultdict
from rdkit import Chem
from rdkit.Chem ... |
5b163b9c34b5029048eee5c605408c2fe7cfce61713bd2045beb5199e6382301 | Python | 37,977 | 861 | import inspect
import logging
import math
import re
from collections.abc import Callable
import numpy as np
import omegaconf
import torch
from ignite import distributed as idist
from ignite.engine import Engine, Events
from ignite.handlers import ModelCheckpoint, ProgressBar, TerminateOnNan, global_step_from_engine
fr... |
a4bcbc978a9a8e3c4ce6e2be29c0ea8095ab3174ce8b362674a97598ea6c0a61 | Python | 38,230 | 847 | """
signal processing functions
"""
import numpy as np
from scipy.signal import butter,filtfilt
import h5py
from lib.data import *
def butter_lowpass_filter(data, cutoff, fs, order):
nyq = 0.5 * fs
normal_cutoff = cutoff / nyq
# Get the filter coefficients
b, a = butter(order, normal_cutoff, btype='low... |
9dfe218cb52eb5168f6360361a74ad19e3fb6a6d6f35a50bef2e444bdb9c85c0 | Python | 38,614 | 785 | """Interfaces for SHIVA project deep learning segmentation and prediction tools."""
import os
import glob
import shlex
import json
from shivai.utils.misc import md5
from nipype.interfaces.base import (traits, TraitedSpec,
BaseInterfaceInputSpec,
... |
adacf09fbfd5016cc10e0bd13c2a4a505f3ff6707d24333076cdb45c1d994fef | Python | 38,736 | 839 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import math
import warnings
from typing import Dict, Literal, Optional, Union
import torch
from torch import Tensor
from torch.distributions import Distr... |
02c1db285a96817415f2cd491a08fa92871585aadd54eb0599a5557ca0032799 | Python | 38,749 | 976 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 6 14:19:20 2021
@author: baris
"""
from neural_coding import load_spikes, rate_n_phase
from perceptron import run_perceptron
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from sklearn import decompo... |
733f871d844779a316ad1d743a96f2b8088bc5a8c465f250cbeba5277bf277da | Python | 38,781 | 1,054 | # SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: MIT
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without res... |
ae9e243041338bbc8f73d144aa9047a194dbfad2dd43c9cd2277b0758a3a2114 | Python | 38,873 | 677 | #!usr/bin/env python
#coding:utf-8
"""
@author: Haidong Zhang
@contact: haidong_zhang14@yahoo.com
@time: 2021/1/9 15:28
@project: MalariaDetection
@description:
"""
from keras.layers import * #For adding convolutional layer
from keras.layers import Dense, ZeroPadding2D, BatchNormalization, Activation ... |
e2a30fab4ac6f306d95a35ef6a27c1fdadf8b48e35a93be1b5789922f2f1d59e | Python | 38,906 | 677 | #!usr/bin/env python
#coding:utf-8
"""
@author: Haidong Zhang
@contact: haidong_zhang14@yahoo.com
@time: 2021/1/9 15:28
@project: MalariaDetection
@description:
"""
from keras.layers import * #For adding convolutional layer
from keras.layers import Dense, ZeroPadding2D, BatchNormalization, Activation ... |
04c9d522b7c8a60a6ba40ac043ab7cfae4a95158585fef76c6b0cd699db1e43a | Python | 38,908 | 1,041 | import sys
import os
import math
import p4.func
from p4.var import var
from p4.tree import Tree
from p4.p4exceptions import P4Error
class Trees(object):
"""A bunch of trees, all with the same taxNames.
This class would be good for doing things that you might want to
do with a bunch of trees rather than ... |
34816c970e7f2bff66119af16f9655769582e89d0ce125cc24afc8daa30bd568 | Python | 39,065 | 941 | import glob
import math
import os
import random
import shutil
import time
from pathlib import Path
from threading import Thread
import cv2
import numpy as np
import torch
from PIL import Image, ExifTags
from torch.utils.data import Dataset
from tqdm import tqdm
from utils.general import xyxy2xywh, xywh2xyxy, torch_di... |
73d520c3f25b784a1518d24fbf2d87da3aee8e8a46de10318b1820bfcd0bbb77 | Python | 39,177 | 976 | """GPU-specific tests for AIMNet2 calculator.
All tests in this module require CUDA and are marked with @pytest.mark.gpu.
Run with: pytest -m gpu
"""
import warnings
import pytest
import torch
from conftest import CAFFEINE_FILE, CIF_SPIRO, TAXOL_FILE, load_mol
from aimnet.calculators import AIMNet2Calculator
from a... |
930c6624d3adba5d582e3517895e66ae6fcd09eb9cd775261af1b9d8fcc20267 | Python | 39,180 | 940 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import numpy as np
import pandas as pd
from scipy.stats import spearmanr
from scipy.stats import rankdata
import seaborn as sns
from sklearn.decomposition import PCA
from sklearn.preproces... |
8e55fbd1726f1588488b1cd133980b539b4605b94686bbc6d8315b70262aba87 | Python | 39,275 | 1,062 | import logging
import os
import re
import json
import nibabel as nib
from nibabel.filebasedimages import ImageFileError
import numpy as np
import pandas as pd
import sys
from subprocess import run
import datetime
import zipfile
import matplotlib.pyplot as plt
import abc
from datetime import time
from nilearn.plotting i... |
4a41ba600b48b1c628b7c21872629080e5c35cd77ff7791d72a4e135e1b33308 | Python | 39,353 | 733 | #!/usr/bin/python
import os
import sys
import numpy as np
import pandas as pd
import argparse
from sklearn.metrics import mean_squared_error, r2_score
from sklearn.preprocessing import MinMaxScaler
import optuna
from optuna.samplers import TPESampler
import joblib
import random
import wandb
random.seed(4)
#import te... |
d10741776ec42388eb1e44c1c943ffa955910c351d56728c2cb372c3026026d5 | Python | 39,368 | 678 | '''
File with configurations to run MLpipeline() class from MLpipeline.py on the IMAGEN data.
This configuration was used for Evert's thesis' experiments and serves as an example for how to
configure the MLpipeline class and run it.
'''
import os, sys
from glob import glob
from os.path import join, isfile
import numpy... |
8706c510c22081d91ce2997f81dcd680e6e4481450f8f19dba5469ecc8cdd902 | Python | 39,409 | 1,382 | #!/usr/bin/python
# -*- coding: UTF-8 -*-
from __future__ import absolute_import
from __future__ import with_statement
from __future__ import division
from __future__ import nested_scopes
from __future__ import generators
from __future__ import unicode_literals
from __future__ import print_function
"""
``util.py``: Mi... |
1a1c376069a5a9c09c41acca75da95a1860a3d1584891c7e51df35fd97cd07d4 | Python | 39,707 | 844 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import Conv2d, Linear, build_activation_layer
from mmcv.cnn.bricks.transformer import FFN, build_positional_encoding
from mmcv.runner import force_fp32
from mmdet.core import (bbox_cxcywh_to... |
871d4678fb7ddb7c74203dc8f4f83b85fdfc038ec4a64109df90d98ec66eaf1e | Python | 39,777 | 1,015 | from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import numpy as np
import math
from itertools import chain
from typing import Union
from Bio.Phylo.BaseTree import Tree
from .ambiguity import (
ambiguity_map,
ambiguity_symbols,
is_nucleotide_alphabet,
... |
83a2db7cb82dc4d762b57a27b61cd4b53110d837a6fab3ddbd3bfa53c200d95a | Python | 39,803 | 815 | # coding=utf-8
# Copyright 2018 The Open AI Team Authors and The HuggingFace Inc. team.
#
# 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
#
# ... |
b2deec69633a0b4202dc699345286b712c271cbc3a71b40951b09d3eb6e57912 | Python | 39,822 | 1,052 | import utils
from os.path import join, isfile, split, splitext
from os import listdir
import logging
import study_analyzer
import sqldbutils as db
import json
import random
import re
import ann_post_rules
import multiprocessing
from analysis.semquery import SemEHRES
class BasicAnn(object):
"""
a simple NLP (N... |
36caaa9f6e4998c5ae7586f896942cf098e55afe3670e31a2f1a26bcc25f1a77 | Python | 39,934 | 921 | import math
import random
from functools import partial
from typing import Callable, Dict, List, Optional, Tuple, Union
import numpy as np
import torch
from Bio.Align import MultipleSeqAlignment
from torch.distributions import Categorical, Distribution
from selbstaufsicht.utils import lehmer_encode
# TODO task sched... |
441d1cae82faa6f64d8a40f8183b410d5ae071b76b0776cf838dc16cba960d32 | Python | 39,961 | 993 | # Copyright (C) 2023-2025 ETH Zurich, Marc Lehner and other DASH contributors.
import gzip
import io
import os
import pickle
from collections import defaultdict
from enum import Enum, auto
from pathlib import Path
import numpy as np
import pandas as pd
from PIL import Image
from rdkit import Chem
from rdkit.Chem impo... |
56c40aaea3a777f3ef02d9b140f4e35fd191553add594ab14171c92585b193e4 | Python | 39,980 | 971 | # libraries
import argparse
import sys
import os
os.environ['QT_QPA_PLATFORM']='offscreen'
import re
import numpy as np
import pandas as pd
pd.options.mode.chained_assignment = None # change from default "warn"
import ete3
import logging
# argument parser
arp = argparse.ArgumentParser()
# Add the arguments to the pa... |
6b52395859c2ca079aa79d569763234788034de5b1ade657521ba59f4167faaa | Python | 40,241 | 1,071 | # Copyright (c) OpenMMLab. All rights reserved.
from abc import ABCMeta, abstractmethod
import cv2
import mmcv
import numpy as np
import pycocotools.mask as maskUtils
import torch
from mmcv.ops.roi_align import roi_align
class BaseInstanceMasks(metaclass=ABCMeta):
"""Base class for instance masks."""
@abstr... |
fb668cd07e73379897a58bc36a4fd49b496441082215e07bf6306a192c23323c | Python | 40,437 | 780 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, 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 cop... |
e8c7e0c2a53ade0d7687f6b33ac95c6c0e3c66d036595558a7f01a50afac14c9 | Python | 40,550 | 894 | # -*- coding: utf-8 -*-
"""
Created on Sun Jul 25 23:58:42 2021
@author: fhu14
Methods for plotting SKF files for a directory of SKFs
We are generally more interested in the functional form of the functions
than the values attained. For this reason, the x-axis is plotted with
more granular information than the y-ax... |
7190cdafd85cc1caaf145e29db4e0670f61d06a477c07ae50458bc06987305d2 | Python | 40,732 | 713 | import copy
import copy
import json
import logging
import pickle
import numpy as np
import torch
import torch.nn.functional as F
import torch.utils.data as data
import torchvision
from torch.autograd import Variable
from torchvision import datasets, transforms
from .datasets import MNIST_truncated, EMNIST_truncated, ... |
afd9e3cee6b6fb12c2f5721c72c32126573190564140a6dc088e874380306ea5 | Python | 40,752 | 812 | import pandas as pd
from A_config import a10_config
import os
import sys
import glob
import calendar
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from mpl_toolkits.axes_grid1 import make_axes_locatable
import skill_metrics as sm
from matplotlib.patche... |
dfdd52fc88a53c4f888649e15d8a724a5a3dcdd17343e2147d4212f93b942afa | Python | 41,155 | 1,041 | from __future__ import annotations
import os
import re
from typing import ItemsView, KeysView, ValuesView, Iterable, Tuple, Union, Dict
import numpy as np
import pandas as pd
from numpy.polynomial import Polynomial
from scipy.interpolate import PPoly, interp1d, CubicSpline, InterpolatedUnivariateSpline
from .consts ... |
a87464e35f30d2045fd71e2cd31b25dd7ae60ca2b9061578e20df5a5d682833a | Python | 41,640 | 921 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 28 13:40:17 2020
@author: Frank
Module for writing skf files, which are basically text files that adhere
to a specific format as described in the slater-koster file format document
Right now, the writer only handles simple format since we are not doing
angular momenta u... |
7c8e32e901443a9ada0863abeff6b1d0279279cab3d2abe40bdf1bd58a49e0f6 | Python | 41,659 | 1,158 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
from __future__ import annotations
import io
import warnings
from dataclasses import asdict
from typing import Tuple, Union
import pytest
import torch
i... |
faf785d868e0f758a27cc621c238a762e1c870328ac104e178d8c7f9db9b9159 | Python | 41,786 | 955 | '''
* Copyright (c) 2022, salesforce.com, inc.
* All rights reserved.
* SPDX-License-Identifier: BSD-3-Clause
* For full license text, see LICENSE.txt file in the repo root or https://opensource.org/licenses/BSD-3-Clause
* By Junnan Li
* Based on huggingface code base
* https://github.com/huggingface/transformer... |
2bce58a565ce88507105903d03400996e143ad5b1d4574cf5c900808c214534f | Python | 41,878 | 1,056 | import itk
import numpy as np
import random
import typing
import re
import json
import pickle
from pathlib import Path
import os
from glob import glob
import matplotlib.pyplot as plt
import pkgutil
from usqc.util import overlay, get_iterator_setup, add_to_group
from usqc.data import get_files
'''
Label-to-pixel value ... |
8967700d45fb0045dba439a67bd57eac740edada8a91d9b6117bfbe7dbbdbf71 | Python | 42,416 | 857 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 8 18:19:17 2021
@author: yaron
(Frank): Made some changes to add_dftb and load_ani1 (documentation and path fixing)
TODO: More options in the code to eventually handle non-zero Fermi temperatures.
Analysis pipeline:
1) get test dataset
... |
730f237fe2e899a6da0df6a042ce7fb1ae04d02edfa5d1c128f782f050e1276f | Python | 42,550 | 961 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 17 12:55:20 2021
@author: baris
"""
from neural_coding import load_spikes, rate_n_phase
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import pickle
from scipy.stats import pearsonr, spearmanr
import c... |
9bdc263649ceca08fae1c979552e20a148f2f732aa5a6f1b7d6191787b7d4596 | Python | 42,593 | 1,104 | import os
import numpy as np
import tensorflow as tf
import tensorflow.experimental.numpy as tnp
import random
from lib.commons import *
import threading, queue
import concurrent.futures
import multiprocessing
import urllib.request
import time
import random
import itertools
import math
import tqdm
import nibabel as... |
a6629a9dc8515b596ad21b41bbc0e21f20673fe8c1f13d7f75f8114a1a8866a8 | Python | 42,614 | 1,231 | # Copyright (C) 2013 Oskar Maier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in th... |
3e4cfde69bdc6ece5acce3dc284b332bfc13f32c8cea100ced62c973b76264f4 | Python | 42,669 | 1,180 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
from __future__ import annotations
import warnings
from copy import deepcopy
from dataclasses import asdict
import numpy as np
import pytest
import torc... |
5eda037b0aa46e181eb0d701ad63058c2c05562abbd3726f9e48db2d5d06f4fe | Python | 42,673 | 929 |
__author__ = "Grzegorz Chojnowski"
__date__ = "26 May 2021"
import os,sys,re
from shutil import which
import subprocess
from scipy.special import erf,erfc
from scipy import stats
import numpy as np
import gzip
import math
import tempfile
sys.path.insert(2, '..')
try:
from doubleHelixLib import cmatch_rna as ... |
566d8bad54d9f0a85bbadc21c1edbe27026061500f9512f341657aced8ec7edb | Python | 42,682 | 1,096 | import sys
import os
import gzip
import argparse
import numpy as np
from itertools import product, groupby
import pysam
import util
import snptable
import tables
MAX_SEQS_DEFAULT = 64
MAX_SNPS_DEFAULT = 6
class DataFiles(object):
"""Object to hold names and filehandles for all input / output
datafiles"""... |
130748b89e746565a61ccf60603a998c7c3ca2c6c26d8647726b83cce8213b5b | Python | 42,897 | 907 | import PySimpleGUI as sg
import numpy as np
import sys
from Analysis_types.Whole_recording import extract_event_data_from_cols
from Post_processing.FED3_post_processing import FED3_post_processing
from Post_processing.Peri_events_post_processing import Peri_events_post_processing
from Statistics.Statistics_GUI im... |
5b3173bc990c6b7e02d394b15d7b73c3cf23ee33a9794d379ecda2fdbf32a0fb | Python | 43,076 | 1,117 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import math
import warnings
from typing import Callable, Literal, Optional, Union
import torch
from torch import Tensor, nn
from sbi.neural_nets.estimat... |
97902f6555d48a60501429c294a901b6fba94f5d062c3d9b973782c1eb4eb570 | Python | 43,375 | 998 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 23 12:29:15 2022
@author: baris
"""
import pickle
import numpy as np
# import seaborn as sns
import pandas as pd
from phase_to_rate import grid_model
from phase_to_rate.figure_functions import (_make_cmap, _precession_spikes,
... |
f0977c8a0424d66008f0cba698d7057bb1cbda70439f89592688410650c03ca6 | Python | 43,474 | 1,018 | # Copyright (c) OpenMMLab. All rights reserved.
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule
from mmcv.runner import BaseModule, ModuleList, force_fp32
from mmdet.core import build_sampler, fast_nms, images_to_levels, multi_apply
from mmdet.core.... |
292a365a07ee4430655f929992e7ab8ccbae8bb59c4a55ccd36ed0971a6e9fc2 | Python | 43,660 | 1,283 | #!/usr/bin/python
# -*- coding: UTF-8 -*-
import sys
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from numpy import *
from lgcpspatial.util import *
import traceback
import scipy.linalg
from scipy.sparse.linalg import LinearOperator
from scipy.sparse.linalg ... |
b3ed051cc113ed4fa580f30cd44333b69a7a6f8e0b31a0050246b13099d1e31b | Python | 43,686 | 1,138 | import sys
import csv
import random
from p4.tree import Tree
from p4.func import read
from p4.var import var
from p4.p4exceptions import P4Error
from p4.reducedstrictconsensus import Intersection, TreeBuilderFromSplits
class SuperTreeInputTrees(object):
def __init__(self, inputTree, distributionTrees=None):
... |
772e2fe3c6b30f1cc03bdfcbb45ccb2ace6dd346930c6f91a347f263e6417c13 | Python | 43,927 | 1,248 | # Imports #
import configparser
import numpy as np
import pathlib
import random
import statistics
import time
import traceback
from Classes.Protocol import ImageButton, ProtocolBase, PreloadedVideo
from kivy.clock import Clock
from kivy.config import Config
from kivy.loader import Loader
from kivy.uix.button import ... |
1ba70959aa50cc0cb115ef3be18cb38fd639a199d83d5a4f3d43af8422096c66 | Python | 44,103 | 1,104 | import p4.pf as pf
import sys
import random
import math
import p4.func
from p4.var import var
from p4.p4exceptions import P4Error
import numpy
class BigQAndEig(object): # not used
def __init__(self, dim, comp, rMatrix):
self.dim = dim
self.comp = comp
self.rMatrix = rMatrix
self.... |
f58fb51fce6d7d4e85d38996b0c811907ba77fdc00b01472252acf73171b2caa | Python | 44,423 | 459 | import argparse
import importlib
import h5py
import numpy as np
import os
# import plotly.graph_objects as go
import torch
from datetime import datetime
# from plotly.offline import plot
from tqdm import tqdm
# from utils import MetricTracker
# from utils.clean_noise import CleanNoise
# from data_loader.general_data... |
113b1392061eade8eb2bd3485ab778308edfac9c1e3134697771cef459056251 | Python | 44,970 | 1,193 | import time
from typing import Callable, Tuple, Union
import numpy as np
import torch
from numpy import ndarray
from torch import Tensor
from .utils import *
class DistanceRuleSimulator:
"""Simulate Peters' rule with the dense structural model.
We define new features, e.g., number of common cubes for each ... |
162872a0eb620195392bd42029363ad7faa299facf1dc58bda1caa2329833f91 | Python | 45,129 | 781 | #!usr/bin/env python
#coding:utf-8
"""
@author: Haidong Zhang
@contact: haidong_zhang14@yahoo.com
@time: 2021/1/9 15:28
@project: MalariaDetection
@description:
"""
from keras.layers import * #For adding convolutional layer
from keras.layers import Dense, ZeroPadding2D, BatchNormalization, Activation ... |
72813bff72d4a77f2cbbf17b854efd5c0a3ca50c92a37e47f6bf268dbd65fd3d | Python | 45,140 | 629 | # =============================================================================
# Created at:
# EMBL Hamburg
# Author:
# Grzegorz Chojnowski - gchojnowski@gmail.com
# =============================================================================
stem_pdb_string_3bps = """\
REMARK 3DNA v2.1 (c) 2012 Dr. Xiang-Jun L... |
8974b12c36b1cbd2eba367cf30a4c84e2471e3dbbf73ddb2c78d1900ad416135 | Python | 45,239 | 1,393 | #!/usr/bin/python
# -*- coding: UTF-8 -*-
"""
Plotting helpers copied from
``neurotools.graphics.plot``, and some new
routines to reduce notebook clutter.
"""
import os
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from numpy import *
from matplotlib.pyplot import *... |
540c1847f0d4fff08ba70c3e2da29b00e2b4c833c49c968ab44e580e86054799 | Python | 45,277 | 1,351 | #!/usr/bin/python
# -*- coding: UTF-8 -*-
"""
posterior.py: Subroutines for further analysis of the posterior rate map returned from Gaussian process inference.
"""
# Load a Matlab-like namespace
from numpy import *
from scipy.spatial import ConvexHull
from numpy.linalg import norm,LinAlgError
from lgcpspat... |
4b7c08f7d196143a8499a3220864f2efde5ced7165c94a71d5327fdc84ad30f8 | Python | 45,467 | 930 | """
Utilities relating to genetic codes.
date: 25/08/2016
"""
import sys
import copy
import warnings
from itertools import combinations, product
import operator
from Bio.Data import CodonTable
from p4.p4exceptions import P4Error
def formatwarning(message, category, filename, lineno, line):
return "%s:%s: %s:%s" % ... |
14b4cbd8ce362552f0b3fb83fde42d45290847550b43860cf079c97c7b1878c8 | Python | 45,716 | 1,069 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import numpy.random as npr
import copy
from functools import partial
from contextlib import contextmanager
from lib.model_zoo.common.get_model import get_model, register
from lib.log_service import print_log
version = '0'
symbol = 's... |
8fb420e52b960efdd7b564753fe69788f65d7ad29c76a914e11228f0522ff348 | Python | 45,828 | 866 | """CUDA-graph replay of repeated ``AIMNet2Calculator.eval`` calls.
``AIMNet2Calculator.eval`` asks ``CUDAGraphCache.eval`` first; ``None`` means "not handled" and the regular code path
runs unchanged.
Handled calls (all of):
* CUDA device; closed-shell AIMNet2 model (``d2features``, one charge channel) with the defa... |
4567106f70e8afdd68a3ece3cc93abbf9253928ed4fd78c73914d1402a0c1eb7 | Python | 45,887 | 709 | import torch as th
from torch.nn import functional as F
import torch.nn as nn
import numpy as np
from torchdiffeq import odeint
from latentvelo.models.velocity_field import VelocityFieldReg
from latentvelo.models.modules import create_encoder, create_decoder, MLP, GCN
from latentvelo.utils import normalize, sparse_m... |
d063c73cb09abc7ae8aca504026c30b46db99d6fd78aa91e2e26c91993d777f9 | Python | 45,913 | 1,159 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import warnings
from typing import Sequence
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import (build_activation_layer, build_conv_layer,
build_norm_layer, xavier_init)
from mmcv.cnn.bricks.registry i... |
84e61d6757b8a55cf410904a2c36cc7299b8b10ee3d9fdfafeb39921f2393538 | Python | 46,042 | 1,311 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
"""Typed dataclass configs for the estimator families.
The per-model configs are how a model is picked and configured: one small class
per model, holding... |
bb631d89a0dc60959edeac43efe05de5fb0af3b3acee21b863097d9819f8140d | Python | 46,184 | 738 | # Copyright (c) OpenMMLab. All rights reserved.
import itertools
import logging
import os.path as osp
import tempfile
import warnings
from collections import OrderedDict
import numpy as np
from mmcv.utils import print_log
from terminaltables import AsciiTable
from .builder import DATASETS
from .coco import CocoDatase... |
604315c2ba8618719e1d24feaaaf43ac38296820ec7436c702994d4f95eec023 | Python | 46,486 | 1,432 | import sys
from pathlib import Path
import rich_click as click
from rich.console import Console
from rich.padding import Padding
from rich.panel import Panel
import genomad
from genomad.utils import get_n_available_cpus
CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
click.rich_click.USE_RICH_MARKUP = Tr... |
e11271c316a4368596f9d93724712cb05cd6da0fae6bdfebf653a57a7086fb2e | Python | 46,499 | 1,330 | import base64
import gzip
import json
import lzma
import struct
import types
import zlib
from hashlib import sha256
from pathlib import Path
import pytest
from clipkit.ecomp.reader import (
HEADER_MAGIC,
LEGACY_HEADER_STRUCT,
METADATA_COMPRESSED_MAGIC,
METADATA_CODEC_VERSION,
METADATA_SUFFIX,
... |
9a146e2dc9101593ae94108778d10ae4d2ce97403d88f3bcd8362d76de2d48a0 | Python | 46,604 | 1,022 | u"""
Module for recoding matrices.
date: 25/08/2016
"""
import sys
import os
import subprocess
import re
import copy
import warnings
from Bio.Data import CodonTable
from p4.alignment import Alignment
import p4.func
from p4.var import var
from p4.p4exceptions import P4Error
from p4.func import read
from p4.code_utils im... |
07b41c6b382b7a046baa8dc203f1300d74cd3dec9aa369c0dbb8ff89ed1e5bc0 | Python | 46,998 | 1,016 | # Author: Fabi Prezja <faprezja@fairn.fi>
# Copyright (C) 2023 Fabi Prezja
# License: MIT License (see LICENSE.txt for details)
import glob
import os
import sys
import numpy as np
import tensorflow as tf
from sklearn.utils.class_weight import compute_class_weight
from tensorflow.keras.callbacks import EarlyStopping
f... |
0a9b47acbec1d3e604f42f75dc79dec525c6136ed0c3875fa9b369c28ecc7a51 | Python | 47,039 | 1,214 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import random
import cv2
import numpy as np
from mmpose.core.post_processing import (get_affine_transform, get_warp_matrix,
warp_affine_joints)
from mmpose.datasets.builder import PIPELINES
from .shared_transform impo... |
c9954fa41f06764c919f4901c642a2ea84d632069e988a2c448516e8196a1ba7 | Python | 47,250 | 1,134 | import os
import argparse
import json
from pathlib import Path
import tqdm
import glob
import multiprocessing
import multiprocessing.dummy as mp
import numpy as np
import librosa
import pyroomacoustics as pra
import soundfile as sf
import sep.helpers.utils as utils
from sep.helpers.constants import SPEED_OF_SOUND
# ... |
cd9bdb8f0af453f139f0c71b3624e2b9b64e6c06cc6b4fac9e2c3df1f1310c30 | Python | 47,265 | 1,177 | # Copyright (c) OpenMMLab. All rights reserved.
import mmcv
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule
from mmdet.core import InstanceData, mask_matrix_nms, multi_apply
from mmdet.core.utils import center_of_mass, generate_coordinate
from mmdet... |
7c8d5b554f59828313a5e9dbe1cfe3e2c4a67ea25c6025a257cb5b59660005d9 | Python | 47,403 | 1,062 | import numpy as np
import pandas as pd
import math
import seaborn as sns
import matplotlib.pyplot as plt
from scipy.stats import linregress
import traceback
import shelve
import pyabf
from utils.calcium_traces import get_pos_y, get_pos_x
from utils.groupsCells import get_cells_group, get_cell_side, get_cells_group_adde... |
1cdc8799f236a050de908db9dc676d97f56b927690f8434268f559fad8e8622b | Python | 47,474 | 1,251 | import numpy as np
import pickle as pkl
import scipy.sparse
import scipy.special
from elements import ELEMENTS
from h5py import File
from matplotlib import pyplot as plt
from deprecated.slakos_deprecated.mio_0_1 import ParDict
from tfspline import spline_linear_model, Bcond, spline_new_xvals
from util import get_datase... |
53a652d342f0a2566fc2d9d9694be1906d43ae012f96be8f0d10354727e0258e | Python | 47,672 | 1,166 | import copy
import warnings
from dataclasses import dataclass
from typing import Dict, List, Optional
import numpy as np
import pandas as pd
from scipy.optimize import minimize_scalar
from scipy.stats import norm
from statsmodels.stats.multitest import multipletests
from .utils._checks import (
_check_benchmarks,... |
7857e6d59ceff818bb1cd303262f2ec9ff278c69fbfc34f6f22680eafa96abf0 | Python | 47,796 | 740 | import torch as th
from torch.nn import functional as F
import torch.nn as nn
import numpy as np
from torchdiffeq import odeint
from latentvelo.models.velocity_field import VelocityFieldReg
from latentvelo.models.modules import create_encoder, create_decoder, MLP, GCN
from latentvelo.utils import normalize, sparse_mx... |
57bdaf414ed098be5e86d1b9801dcb53bfd16a11969a83cb25c130d9045e63a3 | Python | 47,878 | 1,289 | # -*- coding: utf-8 -*-
"""HiFi-GAN Modules.
This code is based on https://github.com/jik876/hifi-gan.
"""
import copy
import logging
import numpy as np
import torch
import torch.nn.functional as F
from parallel_wavegan.layers import CausalConv1d, CausalConvTranspose1d
from parallel_wavegan.layers import HiFiGANR... |
0ffb542ecb21d24d18d377e439fa79f26f5d7bf84c7ab79de606d70795070fb0 | Python | 47,936 | 1,293 | # IMPORT STATEMENTS
import cv2
import re
import numpy as np
import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
from matplotlib import pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable, axes_size
import matplotlib.patches as patches
import matplotlib.co... |
79289cf83fb22833ef15ad6e8e97f92276eb92153b3a533e5a2ce7cb0b45c6cf | Python | 48,420 | 1,083 | # Copyright (c) OpenMMLab. All rights reserved.
from logging import warning
from math import ceil, log
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, bias_init_with_prob
from mmcv.ops import CornerPool, batched_nms
from mmcv.runner import BaseModule
from mmdet.core import multi_apply
from ..build... |
048b9737bb3e43ae730a71510545764b2af668988291507b8862fadec3500dfc | Python | 48,921 | 1,020 | """This module contains all parts of the unified extractor for diagrams, labels and reaction conditions"""
import copy
from itertools import product
from math import ceil
import numpy as np
import json
import os
import re
from typing import List, Tuple, Union
import warnings
import cv2
from matplotlib import pyplot as... |
14b09774aafb4126f9bb6d92bbc9eaf9f7e69abc09a0182361c8614b71c50856 | Python | 49,039 | 1,014 | # -*- coding: utf-8 -*-
"""
Created on Sun Nov 1 23:15:17 2020
@author: Frank
"""
'''
Functions for writing and handling h5 files
Note: to go back from bytestring to normal string, you have to do
x.decode('UTF-8') where x is the byte string representation
With this method of working with h5 files, only ... |
432e98c2b4985fedecc6eab414f535d49f4c8ded0bf0076595db38e500b59143 | Python | 49,143 | 1,244 | #! /usr/bin/env libtbx.python
# -*- coding: utf-8 -*-
# =============================================================================
# Created at:
# International Institute of Molecular and Cell Biology in Warsaw, Poland
# Author:
# Grzegorz Chojnowski - gchojnowski@genesilico.pl, gchojnowski@gmail.com
# ===========... |
2a3ef2a5a3d36c59b4cf206f4af1738f8e1047ca2850124ab788ad313a43e738 | Python | 49,353 | 1,236 | #! /usr/bin/env libtbx.python
# -*- coding: utf-8 -*-
# =============================================================================
# Created at:
# International Institute of Molecular and Cell Biology in Warsaw, Poland
# Author:
# Grzegorz Chojnowski - gchojnowski@genesilico.pl, gchojnowski@gmail.com
# ===========... |
5bf18220109082ed9bb93274874ab1d1f245637e301a8d34e9e7655f40c3afca | Python | 49,355 | 1,303 |
__author__ = "Grzegorz Chojnowski"
__date__ = "21 Apr 2021"
import sys, os, re
# it seems that real_space_refinement_simple
# supports greedy multiprocessing, that for simple,
# and fast single-sc fitting makes no good
os.environ["OMP_NUM_THREADS"] = "1"
ROOT = os.path.dirname(os.path.realpath(__file__))
impo... |
f0d92e427fa8064eef04eb9aa7a539605a634d1b70818b1c9a1f52fdcae597f6 | Python | 49,460 | 1,171 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import inspect
import warnings
from functools import partial
from math import ceil
from typing import Any, Callable, Dict, Literal, Optional, Union
from wa... |
2603b6e6c8d4af8552c5ee86171ec42618ce45d4203012c96c65a21b3315ffba | Python | 49,689 | 742 |
import h5py as h5
import numpy as np
import sys
import ArgParser as argp
from scipy.signal import find_peaks
import PatchAnalPlots as pu
import spike_utilities as su
HEADSTAGE_V={'H1':'_S2_', 'H2':'_S4_'}
HV_VAL_KEY={v:k for k,v in HEADSTAGE_V.items()}
HEADSTAGE_I={'H1':'_S1_', 'H2':'_S3_'}
CURRENT_THRESH=5e-12 #det... |
5b09a23926c80091649f4eb43050339be3a9d749d1e6c68b7c0b7b5d301f9b7e | Python | 49,795 | 1,070 | ############################################
# imports
############################################
import os
import shutil
import unittest
from pathlib import Path
from typing import Any
import pandas as pd
from Bio.SeqUtils import MeltingTemp as mt
from effidict import EffiDict, LRUReplacement, PickleBackend
from ... |
26d05058477836c143a434ec5a47f37db89932aa3995ddc3f3e6dd7d130b15b5 | Python | 50,409 | 1,507 | #!/usr/bin/python
# -*- coding: UTF-8 -*-
"""
heading.py: Subroutines used in
``example 5: heading dependence``.
Some of these routines overlap and will likely be
merged in a later clean-up.
"""
import warnings
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from nump... |
0ae5a7d463ede8ab2fb42708a94d367fecbe66d2723664be737e56efe824805d | Python | 50,496 | 1,350 | import itertools
import numpy as np
import os
import pickle as pkl
import scipy.sparse
import scipy.special
from elements import ELEMENTS
from h5py import File
from matplotlib import pyplot as plt
from deprecated.slakos_deprecated.mio_0_1 import ParDict
from tfspline import spline_linear_model, Bcond, spline_new_xvals
... |
b00ca7f2be4390e958f253088cc0414ec988d12eb839bb2f0823d1c70b898f3c | Python | 50,671 | 1,699 | import sys
import os
import re
import json
import requests
from PIL import Image
try:
from StringIO import StringIO ## for Python 2
except ImportError:
from io import StringIO ## for Python 3
import pandas as pd
import numpy as np
import bitarray
import math
from matplotlib import pyplot as plt
from lifelines i... |
e71267db2b5c2f7ca149a6e13f3f2a1cac2589bd72706d7282260b90039dbb53 | Python | 50,786 | 1,158 | ############################################
# imports
############################################
import os
import shutil
from pathlib import Path
from typing import Any
import yaml
from pydantic import ValidationError
from oligo_designer_toolsuite.config.pipelines.oligo_seq_probe_designer import OligoSeqProbeDesi... |
ecd4860507c359c6d64dcb382b34d3b385874f7a8b7b5873c719fadd16e55839 | Python | 50,941 | 1,303 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import warnings
from dataclasses import dataclass
from enum import Enum, auto
from typing import Any, Callable, Dict, List, Optional, Tuple, Type, Union
... |
433527059613f2c4958a8b327b56c667ecc8774da4064fa0eaa30db73100abe6 | Python | 51,045 | 1,213 | # -*- coding: utf-8 -*-
"""
@author: yaron
The function create_data_set(geom_list, data_list, parDict) creates the data
needed for the DFTB model.
geom_list is a list of Geometry objects
data_list is a list of strings specifying data to be returned
parDict is the parDict object used by the DFTB class
The allowed ... |
7a700985daa0a39d964a78234bfe89175e355a04a7a718038276a30903d14505 | Python | 51,505 | 1,983 | import numpy as np
kernel_1_aggregated = np.array(
[
[
-0.5936652,
-0.06157227,
-1.171423,
0.26309013,
0.03982045,
-0.87791234,
0.47679257,
4.6908383,
-0.16051118,
0.53950083,
... |
2f7017f6c05bceccb1e4c43f46f9ceaee59b3fd0b0cc8a49bc20608b9273aff6 | Python | 51,510 | 1,345 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
import logging
import random
import warnings
from math import pi
from pathlib import Path
from typing import (
Any,
Callable,
Dict,
List,
... |
cbdf8157157dbc6b67f6f944def4c5cadc1dba2ccb791fba1a4d8a45753d802a | Python | 51,731 | 1,717 | # Import
import configparser
import datetime
import os
import pandas as pd
import pathlib
import sys
import time
import threading
import queue
import random
import gc
import math
from collections import Counter
from ffpyplayer.player import MediaPlayer
from kivy.app import App
from kivy.clock import Clock, mainthread... |
91e23a9f11f2e54d1eee69fd9e970af7907b139cf30bf44ee05811f5b4ab67bc | Python | 51,865 | 1,426 | # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
# under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
# pyright: reportIncompatibleMethodOverride=true
import functools
import math
from abc import ABC, abstractmethod
from dataclasses import dataclass
from ... |
49844359de78d6dcde5060ab5ac6544c9e6efbe64abaecc93097973e69998510 | Python | 52,115 | 866 | import torch as th
from torch.nn import functional as F
import torch.nn as nn
import numpy as np
from torchdiffeq import odeint, odeint_adjoint
from latentvelo.models.velocity_field import VelocityFieldReg
from latentvelo.models.modules import create_encoder, MLP, GCN
from latentvelo.utils import normalize, sparse_mx... |
f21e80ef608ee5b6c3ee1063155794a7382d90e3567ccd05f14b1a960d10c758 | Python | 52,639 | 1,065 | # Imports #
import sys
import os
import configparser
import time
import numpy as np
import random
import csv
from kivy.uix.button import Button
from kivy.uix.image import Image
from kivy.uix.label import Label
from kivy.uix.floatlayout import FloatLayout
from kivy.uix.behaviors import ButtonBehavior
from kivy.clock imp... |
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