sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
18ce0230c3e7b8c2f30396c91c541c349f42aeebb49e811fcd4756064f49557f | Python | 62,409 | 1,450 | # -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... |
6a8f2a328dac0d6c121c6f70c7387666b3f64d7f71cf2615ab25f1f05e4d3783 | Python | 62,912 | 1,835 | # Import Libraries
import numpy as np
import pandas as pd
import matplotlib.pylab as plt
from IPython.core.display import display, HTML
display(HTML("<style>.container { width:100% !important; }</style>"))
#load and merge list of patietns from (1) HIS (2) Patients medical records
df2= pd.read_excel("C:\DOCUMEN... |
f27fa726426572bee2757c984c458736e9ba9b11da20161431c5587485b59f12 | Python | 63,151 | 1,408 | #!/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>.
"""Allows controlling a vehicle with a keyboard."""
"""
Welcome to CARLA man... |
9ea0cce9d1c5bf445d0a26fcc824d8d8496a009f05e6fad10c69be36182df4ca | Python | 63,195 | 1,622 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from enum import Enum
from functools import partial
from itertools import product
from numbers import Number
from typing import Sequence
from warnings import warn
import mne
from nibabel.freesurfer import read_annot
import numpy as np
from .._data_obj import ND... |
49e1ec8ee8472849aae2371216f51d316803decad30d876523ae1496710b1e8c | Python | 63,998 | 1,230 | """
PRIDICT pegRNA prediction script including calculation of features.
Additionally, nicking guides (including DeepSpCas9 score from Kim et al. 2019)
and primers for NGS amplicon (based on Primer3 from Untergasser et al. 2012)
are designed in separate output file.
"""
### set parameters first ###
#us... |
50b6335085acd75ac869dfb7c46916f127e6300e613b9d5624c490fcbd9aa025 | Python | 64,690 | 1,248 | '''Tensorflow backend for the slideflow.model submodule.'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import json
import warnings
import shutil
import types
import inspect
warnings.filterwarnings('ignore')
import numpy as np
import tensorf... |
a4d608780f2a017413f26bb14f7d53d6891a2450510fdbcaa3387f40c96ded9a | Python | 64,764 | 2,111 | """The core functionality for supporting Hero search space.
1. Parse a program from string.
2. Execute a program in a given namespace, including both concrete and
abstract execution.
3. Mutate a program.
4. Turn a program to string for visualization and serialization.
The main classes are:
1. Program: the main co... |
8990acded240487fb6920cf1f87382b30d1ab5e856a44ba23c98ef6fab79574e | Python | 64,882 | 1,675 | import inspect
import mmcv
import numpy as np
from numpy import random
from .my_transform import Rotate1
from mmdet.core import PolygonMasks
from mmdet.core.evaluation.bbox_overlaps import bbox_overlaps
from ..builder import PIPELINES
try:
from imagecorruptions import corrupt
except ImportError:
corrupt = No... |
4f32233b16f0fb7f315c3f7280d77470dd89759d15db39c865e735ddb9856f77 | Python | 65,758 | 1,365 | """
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... |
0ced9d18c33373a0d86b24e5b8d4e9b1cc985c22d53ef35ac1c77417808b8558 | Python | 65,831 | 1,919 | """ A module containing the models to be trained on gene expression data """
import copy
import itertools
import pickle
import sys
from abc import ABC, abstractmethod
from collections import OrderedDict
from typing import Union, Iterable, Tuple, Any
import neptune.new as neptune
import numpy as np
import sklearn.line... |
16df97c299334f384c83bf1642afd372c2974ce4c6264f5aafd34c4710515d86 | Python | 65,861 | 1,527 | # -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... |
c2fbb12441303fbc81480cb6c5f8fba326fc1edac30f255fd6d6189bc0be83c6 | Python | 65,904 | 1,528 | # -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... |
ef1721933409d1da1a9aebce287aa3916ffab23d3efa3f6f22f062aaf96823a6 | Python | 65,909 | 1,527 | # -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... |
11935cea72f7d51aae6b69d243aa363a8d0f827111e379239880a7bee9f47430 | Python | 66,001 | 1,768 | """Source reconstruction."""
from __future__ import annotations
import os
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
import mne
from mne.beamformer._compute_beamformer import (
Beamformer,
_proj_whiten_data,
_reduce_leadfield_rank,
)
from mne.beamformer._lcmv import _apply_... |
8c957e201f3c004818f9a9fc205a51d7a100673b73f4904cbc1905b29d3bf07a | Python | 66,001 | 1,182 | # module for processing adjacency matrices in various ways
import pandas as pd
import numpy as np
import csv
import matplotlib.pyplot as plt
import seaborn as sns
import pymaid
from tqdm import tqdm
from joblib import Parallel, delayed
class Adjacency_matrix():
def __init__(self, adj, input_counts, mat_type, pai... |
10e17baff05e3b72515cf8cb3120aadf2219c45989d04e18cf9562958d7c9f84 | Python | 66,046 | 1,468 | #!/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>.
"""Allows controlling a vehicle with a keyboard, focused on fisheye cameras."... |
73870207ed2cecb8d0a381df2292f84338eef9a27aa7bc1baf8a5ae82cfb20e1 | Python | 66,119 | 1,535 | # -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
i... |
c15ec66a2a13434ed09d4067e5b954280b6802280c49c60f09762e6ecbb07df4 | Python | 66,140 | 1,183 | # module for processing adjacency matrices in various ways
import pandas as pd
import numpy as np
import csv
import matplotlib.pyplot as plt
import seaborn as sns
import pymaid
from tqdm import tqdm
from joblib import Parallel, delayed
class Adjacency_matrix():
def __init__(self, adj, input_counts, mat_type, pai... |
a3c4a4a12ff24f6696061cf7f63ab9f6723fe2157176f0e80d0a1e84302946b4 | Python | 66,250 | 1,452 | #!/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>.
"""Allows controlling a vehicle with a keyboard."""
HELP_TEXT = """
Use ARRO... |
c0361385f4c16fdc63c871f094361422f158ca0b5964d90604bfe3ef5508e289 | Python | 66,434 | 1,716 | import os, sys, time, re
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
import random as rnd
import numpy.random as npr
from numpy.random import rand,randn,randint,choice
from scipy.integrate import solve_ivp, odeint
verbose=0
mplotlibcolors=['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd'... |
4a9509d0ba47b0b1ca3586dc0fd20ccf70f2b48d3d93148ae8e9a72f0deaa381 | Python | 66,534 | 1,667 | # 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... |
a413cb08f9362b562427341cce8928ebea459c81e35444bfa4a5e6349eba101a | Python | 66,573 | 1,622 | import logging
import time
import typing
from abc import ABC
from collections import defaultdict
from concurrent.futures import ThreadPoolExecutor
from dataclasses import dataclass
from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union
from urllib.error import HTTPError, URLError
import kgcl_rd... |
00ddc6c1952c5745620a371897ce7b4ddae8011482bdaf5c736f5f60cd2ab5bd | Python | 66,806 | 1,822 | from dipy.align import resample
from dipy.segment.clustering import QuickBundles
from dipy.segment.metric import AveragePointwiseEuclideanMetric
from dipy.segment.featurespeed import ResampleFeature
from dipy.io.streamline import (
load_tractogram, save_tractogram, StatefulTractogram, Space)
from dipy.data.fetcher ... |
3b3e8004d766378f2804baa71186737ce7a03cdc23280637a2e74b490949c9a2 | Python | 66,863 | 1,842 | """ This file contains dataset objects for manipulating gene expression data """
import random
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Sequence, Tuple, List, Union, Set, Dict
import numpy as np
import pandas as pd
import yaml
from sklearn import preprocessing
import utils
def... |
0f3069240cef5e31107d4eb6f7b0c0bdcc58473f2c611b040613326e91f7ecf6 | Python | 67,478 | 1,817 | # -*- coding: utf-8 -*-
"""
A collections of helper functions to work with dataset.
Load benchmark dataset, save and restore model, save and load variables.
TensorFlow provides ``.ckpt`` file format to save and restore the models, while
we suggest to use standard python file format ``.npz`` to save models for the
sake... |
09022f4041536c068a7b08eb3eefcece40e5a015707a8f2dadd78446f957915c | Python | 67,513 | 1,770 | # 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... |
a80d839d11d7140c8be1be581306e24a3526ea00213c9d2f9b3865fae3b4a235 | Python | 67,581 | 1,525 | # ----- IMPORTS and STUFFS -------------------------------------------------------
from re import sub
from sklearn.metrics import *
import firebase_admin
from firebase_admin import credentials, auth, firestore, storage
import pandas as pd
import os
import datetime
import math
from math import *
import urllib.request
im... |
a322e597bfac68ac06f37c04ee7fa3071b4079f500f1b20be2a8f636b503da87 | Python | 68,263 | 1,139 | import torch
import warnings
from abc import ABC
from typing import Iterator
from collections import deque
from torch.utils.data.dataset import T_co
from datasources.datasource import Datasource
from torch.utils.data import Dataset, IterableDataset
from datasources.preprocessing_lib import *
from lab.training_tools imp... |
17a5a1854a825aa7b4fb7f75009f88ea4e7f40df7b1abfd0b6d1ab5604cb94ea | Python | 68,265 | 1,601 | # load seg map, make sure they're aligned with heatmap. Remove neg value in heatmap for fair comparison.
import nibabel
import os
import logging
import glob
import numpy as np
import pickle
from argparse import ArgumentParser
import matplotlib.pyplot as plt
import matplotlib as mpl
from mpl_toolkits.axes_grid1 import... |
75e51aafc865d111896f75bad141b685564f2ab41cf8408744069f58e49a1eab | Python | 68,478 | 1,541 | # ----- IMPORTS and STUFFS -------------------------------------------------------
from re import sub
from sklearn.metrics import *
import firebase_admin
from firebase_admin import credentials, auth, firestore, storage
import pandas as pd
import os
import datetime
import math
from math import *
import urllib.request
im... |
0bdf72954d957996cb51a19608204fb3a0b14ab517ab177372baec52cc9ad5c4 | Python | 68,676 | 1,315 | """NuRec scenes as Cosmos clips: a real place, a real rig, a real drive.
A NuRec artifact (``<uuid>.usdz``) is a Gaussian-splat reconstruction of twenty seconds of
real driving. Everything this module needs is *inside* that zip:
============================ ==========================================================... |
1c8ef89d5fe2d4536aeb7a54ab694992f1a2cd9f651117f5016327e220f1df15 | Python | 68,752 | 1,886 | # Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
(... |
ca5c1a5f5324f1b78bc9ddeecbe009bdefa3a0e73c11802d9a873a90962f12e6 | Python | 69,001 | 1,599 | #### Analysis on experiments
"""
This file performs downstream analysis on the output of the siVAE/VAE.
0. Basic analysis on the siVAE results/ Input dataset
1. siVAE loadings comparison
a.
2. Gene embeddings
a. Geneset analysis: create scatterplot of embeddings annotated with genesets
b. Iden... |
4283d1ee3386d3b165bdcd3d102ef3ff586b929b864362f46a824a8042f94670 | Python | 69,128 | 1,937 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 30 12:56:47 2019
@author: rjovelin
"""
# import modules
import os
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from matplotlib.patches import Patch
from matplotlib.lines import Line2D
from mpl_toolkits.axes_grid1 import make_axes_locatable
impo... |
4513b140960d2c188e2b3e905148526fc8d91dd1ea5658796efc14286f940598 | Python | 69,179 | 1,322 | #!/usr/bin/env python
import pandas as pd
import datetime
from scipy import sparse
import scipy.io
from scipy.stats import zscore, wilcoxon, spearmanr
from sklearn.preprocessing import binarize, normalize
from sklearn import metrics
from itertools import cycle
import os
import pickle
import seaborn as sns
import subp... |
7243147641eb4d38bf1bf0476cae660b2e162822ea488ee1d1b10dc80e45ce02 | Python | 69,237 | 1,562 | import sys
#(2P_date, 2P_genotype, 2P_fly, 2P_recroding, 2P_trim_start_time (s), 2P_trim_end_time (s), CC_fluorescein_recording, confocal_data, confocal_genotype, confocal_fly)
#todo: check which 2P recording, cc512, confocal images are representative,
TwoP_recordings_sparseLine_list=[
################ visuall... |
56a51f9cbdcdd768d4cb7fca28d7dd02fcd5e27eb2090ad0c3fcf84c1ac3c184 | Python | 69,332 | 1,541 | import itertools
import torch
from torch import nn
from torch.utils.data import TensorDataset
import torch.nn.functional as F
import numpy as np
import scipy.special as sps
from net_utils import StatefulBase, check_dims, random_weight_init, binary_classifier_accuracy, xe_classifier_accuracy
#%%############
### Hebbia... |
8968bed2d22df111ba3640e9f7dbfa43c90afbbe381cb9da89993be97f31f746 | Python | 69,669 | 1,633 | import sys
import os.path
import platform
import copy
import itertools
#PySide2 imports
from PySide2 import QtCore, QtGui
from PySide2.QtCore import Slot
from PySide2 import __version__ as pyside_version
from PySide2.QtWidgets import QApplication, QMainWindow, QWidget, QGridLayout, QMessageBox, QFileDialog, QAction, Q... |
94eda505a91e65a366480a56e761629315959c40084f726919ba166c6cd28d73 | Python | 69,978 | 2,116 | """Functions to perform spectral analysis."""
import logging
from typing import List, Optional, Tuple, Union
import numpy as np
from scipy import signal
from scipy.signal._spectral_py import _median_bias
from sklearn.decomposition import non_negative_factorization
from osl_dynamics.utils import array_ops
from osl_dy... |
3645fdc1c3ef7b7fdd4655df8cb6b60cbaae0cd435e71d5c3a5e2a79f84272b5 | Python | 70,303 | 1,915 | """Base class for handling data."""
import atexit
import hashlib
import json
import math
import os
import re
import logging
import pathlib
import pickle
import uuid
from contextlib import contextmanager
from functools import partial
from dataclasses import dataclass
from typing import Dict, List, Optional, Tuple, Unio... |
39f78ca7cfdd52bff3205fc6801f5fb841bf7373dfc0b467d86bb084520ec4d6 | Python | 70,343 | 1,260 | #%%
import os
import sys
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
# %%
import sys
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/maggot_models/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
fr... |
f9fb0b5efaecb608f20020afb256c3dcb271258ec1cffb52ac3c976209215c59 | Python | 70,376 | 1,620 | #!/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>.
"""Allows visualising a 2D map generated by vehicles."""
"""
Welcome to CARL... |
6436043c1ab4e6bdb373903ce44b68c22ecd4dd9ca07be68d61006b8cb205973 | Python | 70,962 | 1,876 | """GUI for rejecting epochs"""
# Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
# Document: represents data
# ChangeAction: modifies Document
# Model: creates ChangeActions and applies them to the History
# Frame:
# - visualizaes Document
# - listens to Document changes
# - issues commands to Model
from... |
7d9adb3c3dc68e2e455cb0bf1cd4ded10155fb4e32a0fcd7d42b3000d40f3c94 | Python | 70,983 | 787 | # 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... |
289783392517a0b475484287ba817185ce432176404fe0291cf59f0215cbd9b3 | Python | 71,598 | 2,433 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Document model for formatted text documents
Objects for the abstract representation of a document which can be into
different formats. Currently (incomplete) support for str, RTF, TeX and HTML.
Base classes:
:class:`FMTextElement`
A string (or object w... |
7deba915da0826fccbb28a78d2ae5b8b993e30fcfb6db00f1511685221e32db2 | Python | 71,674 | 1,602 | import math
import torch
import numpy as np
import torch.nn as nn
from pytorch_lightning.loggers import wandb
from torch import Tensor
from typing import Dict, Tuple, Union, Any
import pytorch_lightning as pl
import torch.nn.functional as F
from constants.constants import *
from neural_networks.unet_nilm import quantil... |
7915bfa8f684e8e11ba8ab8ec76dceb5cb602e4c1a2cba95e9683bc22e172e48 | Python | 71,741 | 1,872 | import sys
import re
import statistics
import string
import random
import os.path
import itertools
import copy
from collections import defaultdict, Counter
import numpy as np
import pandas as pd
import copy
import docx
import docx.shared
from docx.oxml import OxmlElement
from docx.oxml.ns import qn
from docx.table impo... |
e48d222464fff9b636d7a4d0ecb39f9af42b51793dc59a230da6d9dfd6d5f4ce | Python | 71,813 | 1,949 | # Obtains the cell threshold, rheobase, resting v, and bias currents for
# steady state v of a cell defined in a hoc file in the given directory.
# Usage: python getCellProperties /path/To/dir/with/.hoc
import cPickle
import csv
import json
import os
import re
import shutil
import string
import urllib
from abc import ... |
77def41a73e97e9aa50952ebccb4db18192f0add548311dd6e2c58ea1640cf82 | Python | 71,934 | 1,561 | import pandas as pd
import numpy as np
from pandas import read_csv
from scipy.ndimage import uniform_filter1d
import csv
from . import utilities
__all__ = ['Test']
class Test:
def __init__(self, filename, filter_size = 20):
self.filename = filename
self.filter_size = filter_size
def set_data... |
3bb87b05f712ac90611481dd91cee64e833b24fab9aa9d4b9c3c8cdd9ad1c28c | Python | 72,134 | 1,528 | # -*- coding: utf-8 -*-
"""
@author: Yuxiu Shao
Network with reciprocal random components;
Full-rank Gaussian Network and Gaussian-mixture Rank-one Approximation
Dynamics
"""
import numpy as np
import matplotlib.pylab as plt
from numpy import linalg as la
# import seaborn as sb
from functools import partial
# from s... |
a4837335d0cd956a0f06583de22e2284777e71527acedad5ba90aa60089cdec3 | Python | 72,393 | 2,122 | # 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... |
6ff57b8957408d5325716e45d6408d5f8a07d1762b87c87c994c8a341458a5a3 | Python | 72,724 | 2,135 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
6072b7a22fabf17c67ff2d8061e42307199de7e7ff7f84bba21b4d4c2cc3dd8c | Python | 73,124 | 1,913 | import csv
import json
import logging
import re
import subprocess
import sys
import tempfile
import unittest
from pathlib import Path
from shutil import copyfile
from typing import Optional
from unittest.mock import MagicMock, patch
import rdflib
import yaml
from click.testing import CliRunner
from kgcl_schema.datamod... |
6a20aa6835f8bb9de12e1f582b6c99717282a5eac9473db67460cc22caf0148f | Python | 74,779 | 1,644 | # -*- coding: utf-8 -*-
import inspect
import tensorflow as tf
from .. import _logging as logging
from .core import *
__all__ = [
'RNNLayer',
'BiRNNLayer',
'ConvRNNCell',
'BasicConvLSTMCell',
'ConvLSTMLayer',
'advanced_indexing_op',
'retrieve_seq_length_op',
'retrieve_seq_length_op2',
... |
f157b4dc334e2b4aee0dfe7256e16f0a81a9d10bb74fe90acdc2f0998662e62d | Python | 75,195 | 1,394 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# We disable pylint because we need python3 compatibility.
from six.moves import xrange # pylint: disable=redefined-builtin
from six.moves import zip # pylint: disable=redefined-builtin
from tensorf... |
a3fcd7c991982358fb7f05c15b9d3eb518ef3d9045b280371d1722ff46252336 | Python | 75,623 | 1,878 | # -*- coding: utf-8 -*-
import tensorflow as tf
from .. import _logging as logging
from .core import *
__all__ = [
'Conv1dLayer',
'Conv2dLayer',
'DeConv2dLayer',
'Conv3dLayer',
'DeConv3dLayer',
'UpSampling2dLayer',
'DownSampling2dLayer',
'DeformableConv2d',
'AtrousConv1dLayer',
... |
7767676f68d742f6771e8fe0911ca9b010861556adb7ecd1e098f34df68c1517 | Python | 76,589 | 1,263 | #!/usr/bin/env python3
"""
File: decon_eqtl.py
Created: 2021/07/12
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 Software ... |
51a83856617a559710492fec1397284c7ca58e5a359e5694e4776e3d62101fd7 | Python | 77,298 | 2,056 | """Command-line interface for CROPro.
CROPro exposes pipelines as subcommands:
- ``cropro crop ...`` -- crop prostate MR images (center/random/stride).
- ``cropro resample ...`` -- resample a dataset's ADC/HBV scans and masks onto
the T2W grid so the sequences are aligned before cropping.
- ``cropro normalize .... |
e5b4be9a9f6e718ef1006ff20b48d063920680a96fb082b83ba0d6c54acf2d81 | Python | 77,651 | 1,710 | #-----------------------------------------------------------------------------
# Copyright (c) 2022--, Bojing Jia.
#
# Distributed under the terms of the GPLv3 license.
#
# The full license is in the file LICENSE.txt, distributed with this software.
#---------------------------------------------------------------------... |
2272eae0548b6ede6457e8852e30b8516248d260ca77d5f4ccdc445dce073cc2 | Python | 78,112 | 1,102 | # Based on (Jurgens et al 2018)
# pylint: disable=line-too-long
# These include manual lexicons defined by Teufel 2006 and Jurgens 2018
# that help identifying the citation intents.
# They also include linguistic patterns and rules that are leveraged as features for the classifier
# From: Jurgens et al. (2018). Measuri... |
8819845d780e4955e05384c9659a971071e342b5f48fe8e17472d44ffb3d3e52 | Python | 78,452 | 1,830 | """
Clustering classes and functions for RACCOON
F. Comitani @2018-2022
A. Maheshwari @2019
"""
import os
import sys
#from shutil import copyfile
import csv
import pickle
import logging
DEBUG_R = 15
""" Suppress UMAP and numpy warnings. """
import numba
import warnings
warnings.filterwarnings(
"ignore",... |
1f78763956fd7bd973ed280ff0a4c33f623d163832b17a903378c41a19f653e3 | Python | 78,864 | 1,387 | import os
import warnings
import torch
import pandas as pd
from typing import Union
from constants.constants import *
from lab.nilm_trainer import train_eval, train_eval_super
from constants.appliance_windows import WINDOWS
from datasources.datasource import Datasource
from datasources.datasource import DatasourceFact... |
b61890a204b3921ada763d70623a1a39f746744a9393d7dc89d02eeae8775135 | Python | 78,970 | 1,414 | """
========================================================================================================================
Network Architect Module
========================================================================================================================
(incomplete documentation)
Classes
-------------... |
85c30e178a9b3c3eb2d6680c768ac3dbbe55fd337ba882009d5adabc9edbe7f3 | Python | 79,432 | 5,176 | import numpy as np
import pandas as pd
import matplotlib.pylab as plt
import openpyxl
pd.set_option('display.max_rows', 50)
pd.set_option('display.max_columns', 100)
pd.set_option('display.width', 1000)
#define name of hospital in databases, this will be used in the future
hospital_name="Emam"
if hospital_name=="Ema... |
050b981c67cabc5cea493a5055114b1a36c448e43655d3528dc0cfff60afa97c | Python | 80,360 | 1,887 | #### Analysis on experiments
"""
This file performs downstream analysis on the output of the siVAE/VAE.
0. Basic analysis on the siVAE results/ Input dataset
1. siVAE loadings comparison
a.
2. Gene embeddings
a. Geneset analysis: create scatterplot of embeddings annotated with genesets
b. Iden... |
eb39139ddcda232d7268d2f15c605412b7aa9d26b74aa42b8c3bb031023a85ad | Python | 80,801 | 2,400 | """Wrapper functions for use in the config API.
All of the functions in this module can be listed in the config passed to
:code:`osl_dynamics.run_pipeline`.
All wrapper functions have the structure::
func(data, output_dir, **kwargs)
where:
- :code:`data` is an :code:`osl_dynamics.data.Data` object.
- :code:`ou... |
6048ed913ac3cdcf528a969743ed25c9fa6e5e87c53e5e88a6e632bc45914353 | Python | 81,917 | 1,669 | # -*- coding: utf-8 -*-
"""
@author: Yuxiu Shao
Sparse EI Network with reciprocal connectivity, Full-rank Gaussian Network and Rank-one Mixture of Gaussian Approximation
Connectivity, Dynamics
"""
''' HELP FUNCTIONS '''
import numpy as np
import matplotlib.pylab as plt
import matplotlib
from numpy import linalg as la... |
12ffd91da2dd09ba7b533ad377100d92b41b1d0cd92d4ca433c7ce8e23fcc423 | Python | 82,976 | 2,742 | """Plotting functions."""
import logging
from itertools import zip_longest
from typing import List, Optional, Tuple, Union
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib
import matplotlib.pyplot as plt
from matplotlib import patches
from matplotlib.path import Path
from mpl_toolkits.ax... |
0dc5eeb78cb3426f968802ea92e1092b26b63032556bba88057fdecd661dc26e | Python | 83,242 | 2,546 | import abc
from copy import deepcopy
import matplotlib.pyplot as plt
from matplotlib import rcParams
import numpy as np
from numpy.linalg import inv
import weave
from weave import converters
from .GIF import GIF
from .Filter_Rect import Filter_Rect_LogSpaced
from . import Tools
from .Tools import reprint
class iGIF... |
1b0a83664a7a26640eb6e66d6edee4a92e2d77d0d826d9a881bbfa6eada3a558 | Python | 83,477 | 2,420 | """Custom Tensorflow layers."""
from typing import List, Optional, Tuple, Union
import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow.keras import (
activations,
layers,
initializers,
regularizers,
)
import osl_dynamics.inference.initializers as osld_initiali... |
e8f26a810a68d86f1c7c7f1b012c681ed3b6d62be938f636b12cb4ac2302ba27 | Python | 83,870 | 1,771 | import os
import sys
import csv
import types
import time
import pickle
import seaborn as sns
import numpy as np
import pandas as pd
import multiprocessing as mp
import slideflow as sf
from tqdm import tqdm
from functools import partial
from slideflow.util import ProgressBar, to_onehot
from os.path import join
from sli... |
a1a8e804ebb0d975ac6e647520835bbbd34e3c5b13ec05fc4ecb5eb97f050023 | Python | 83,910 | 1,831 | """
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... |
555b4b83789ed11f3162df3b845d760280c5ac130008d0c08a7d7755e58e4d57 | Python | 84,040 | 1,994 | #!/usr/bin/env python
"""Module Description: Test the `macs3 hmmratac` command and the public
output functions in MACS3.Commands.hmmratac_cmd.
Most command-line runs use a small synthetic ATAC-seq-like BEDPE file
(open regions full of short fragments, flanked by positioned
nucleosomes, over a sparse background of mon... |
b911638d27d4df17caa2b7754f0eaa7b5d82e9dc10eef916a6f9019b9868ff53 | Python | 84,600 | 2,011 | # SPDX-FileCopyrightText: © 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""
NUREC Integration Module
This module provides the main integration between NUREC (Neural Reconstruction Engine)
and CARLA simulation. It contains classes and functions for:
- Loading and manag... |
fe01d3dcd16362ea13fccf5ee24d7a30487d332c35a1153f6d653022e135728c | Python | 86,672 | 2,317 | # Version: 0.29
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain (Unlicense)
* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3
* [![L... |
90abc30eae82b61943a5c7f1bd1fa1135534d94d86797640fa8e12515de1e087 | Python | 86,853 | 2,333 | # Version: 0.29
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain (Unlicense)
* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3
* [![L... |
1eaec41a4eaf02743888306c3bb18afad3caeba7deda192d8546d1fbfc20b453 | Python | 87,235 | 1,295 | """Implicit generator for 3D volumes"""
import random
from siren.siren import sample_from_3dgrid
import torch.nn as nn
import torch
import time
import curriculums
from torch.cuda.amp import autocast
from .util import gather_points, scatter_points
from .volumetric_rendering import *
class ImplicitGenerator3d(nn.Module... |
16465bd79190a898cbf1c907567a6e70a18752e6959da813e252945b3313f665 | Python | 87,862 | 1,887 | '''This module includes tools to convolutionally section whole slide images into tiles.
These tessellated tiles can be exported as PNG or JPG as raw images or stored in the binary
format TFRecords, with or without data augmentation.
Requires: libvips (https://libvips.github.io/libvips/).'''
from __future__ import abs... |
0ea7db39266661cfb70af7cf3a217fc358535f4b6deb66c96e3723e9a50617ed | Python | 88,157 | 1,836 | import sys
from numpy.lib.type_check import imag
from torch._C import device
from torch.functional import align_tensors
sys.path.append('/apdcephfs/share_1330077/starksun/projects/pi-GAN')
from fid_evaluation import output_images
import numpy as np
import torch.nn as nn
import torch
import math
import torch.nn.functio... |
07e2a82ac30bb49edabb37680f70124331121f198a209d6174d30a7151260199 | Python | 89,079 | 2,237 | from itertools import combinations, product
import itertools
import json
from logging import critical
from multiprocessing import Pool
import os
from typing import Any, Callable, Dict, Iterable, List, Tuple, Union
import logging
from matplotlib.colors import TwoSlopeNorm
import matplotlib.gridspec as gridspec
from pal... |
e3479baaed93e94f16bddd4b620988dac277e00ae9f31ce98d86f63871c8312f | Python | 89,622 | 2,051 | #! /usr/bin/env python3
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 7 14:21:29 2021
@author: Alexandra Vallet
This scritps allow to write slurm files and a batch file in order to launch the PVS simulations on the supercomputer.
The simulations can also be run locally in the docker cont... |
595d55df51b2c53c925e47863e5f23fb9ebc61a2fd5530194bae8a09ad599fa6 | Python | 90,163 | 2,313 |
#!/usr/bin/env python
import os
import cmath
import math
import sys
import numpy as np
import glob
import subprocess
import re
# from matplotlib_venn import venn2
import pandas as pd
from collections import defaultdict
from operator import itemgetter
import matplotlib as mpl
import matplotlib.pyplot as plt
from optp... |
33ef44c11e72c094770aa8727191561efddffd6937823c438c7ca61e4d391bb4 | Python | 90,419 | 2,255 | import tracemalloc
import warnings
from contextlib import nullcontext
import numpy as np
import pytest
import scipy.fft
from nitime.algorithms.spectral import dpss_windows as nitime_dpss_windows
from spectral_connectivity import _backend
from spectral_connectivity.connectivity import Connectivity
from spectral_connec... |
2800b2ed372d2b64b94346dbd18e65c14423dc8561d9176200bd7f5f278223ea | Python | 90,599 | 2,639 | # 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... |
a37f5583db00e4a26c29949a73de550d9b077b3c4f8bd6de35168e4ee8f61b17 | Python | 90,606 | 1,565 | #!/usr/bin/env python3
"""Unit tests for carla_pack.py (standard library only, no engine needed).
python3 Util/ContentPacks/test_carla_pack.py
"""
import contextlib
import io
import json
import os
import shutil
import sys
import tarfile
import tempfile
import unittest
from pathlib import Path
sys.path.insert(0, ... |
82df093e71b3520532131df95bc5915533e71bf91cfbcc68f40081ed4fba5426 | Python | 92,246 | 2,067 | import itertools
import torch
from torch import nn
from torch.utils.data import TensorDataset
import torch.nn.functional as F
import numpy as np
import scipy.special as sps
from net_utils import StatefulBase, check_dims, random_weight_init, binary_classifier_accuracy, xe_classifier_accuracy
#%%############
### Hebbia... |
b2e13dbb8bffbf2b990a18212c093ca910cec37e78fab8f999047df69213922d | Python | 92,426 | 2,515 | # Copyright 2024 Chen Liang
#
# 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 in writing, ... |
45a2514393dafcadbedacf39972319fe072721ae82d00ef384f6f00069bfebe8 | Python | 95,566 | 2,417 | __author__ = 'duarte'
"""
=====================================================================================
Analysis Module
=====================================================================================
Collection of analysis and utility functions that are used by other modules
(Note: this documentation is i... |
9fb39d7310a124df499e45a5de1c401ee014613ed29928d9931235dda3d4e34d | Python | 95,646 | 1,836 | import copy
import queue
import threading
import time
import os
import csv
import shutil
import types
import multiprocessing
import shapely.geometry as sg
import slideflow as sf
import numpy as np
import pandas as pd
from random import shuffle
from glob import glob
from os import listdir
from datetime import datetime
... |
8edc2153c56b81f3ba6da7b91bed21af18a3b70634f19e2d4e6b82bf0ee99222 | Python | 100,405 | 2,571 | """
Compliance tests for multiple interfaces.
See <https://github.com/INCATools/ontology-access-kit/issues/291>_
"""
import json
import logging
import tempfile
import unittest
from dataclasses import dataclass
from pathlib import Path
from typing import Callable, List, Optional
import kgcl_schema.grammar.parser as k... |
4eefed4ae59efe14f30ca04ded0fe2093b273c438c0e8a1c5730b16084baa21a | Python | 103,364 | 3,423 | from oaklib.datamodels.association import Association
NCBI_ASSOCIATIONS = [
Association(
subject="NCBIGene:1956",
predicate="enables",
object="GO:0005524",
property_values=[],
subject_label="EGFR",
predicate_label=None,
object_label="ATP binding",
neg... |
93b6aca621c4ef0e4ec54e97824e532a4a2d1a4b102eee42af6f29a09dfa99ce | Python | 105,720 | 2,258 | import torch
import torch.nn as nn
import functools
from torch.nn import init
from torch.optim import lr_scheduler
# Class components
class DownSample(nn.Module):
"""
SingleConv1D module + MaxPool
The output dimension = input dimension // down_ratio
"""
def __init__(self, input_chan_num, output_c... |
2f4498789f1c5e12a9f35587c0e98d9bb6ecc4190b5050969925df1d4adf38f1 | Python | 106,529 | 1,942 | # Auto generated from ontology_metadata.yaml by pythongen.py version: 0.9.0
# Generation date: 2022-05-29T22:52:46
# Schema: Ontology-Metadata
#
# id: http://purl.obolibrary.org/obo/omo/schema
# description: Schema for ontology metadata
# license: https://creativecommons.org/publicdomain/zero/1.0/
import dataclasses
i... |
2e046c180d018c2dbc3803b77cafcd16bae73cc0f0072c7de2f79596216d0f3a | Python | 107,313 | 2,850 | # -*- coding: utf-8 -*-
# lucam.py
# Copyright (c) 2010-2019, Christoph Gohlke
# Copyright (c) 2010-2019, The Regents of the University of California
# Produced at the Laboratory for Fluorescence Dynamics.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are... |
faac1342b322ec6f97839c0d7c0af9982488f1348a12ebe1c87efbcda27fdff4 | Python | 107,403 | 2,932 | # ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# LAMMPS Development team: developers@lammps.org
#
# Copyright (2003) Sandia Corporation. Under the terms of Contr... |
c5214ce44580f9cdc8b146b7f9dfbecf396627baee07aedd23b498a7cd761b5f | Python | 108,228 | 2,032 | '''
Experiment of randomize model parameters and check heatmap similarity change
Adapted from https://github.com/adebayoj/sanity_checks_saliency/blob/master/src/randomize_inceptionv3.py
'''
from pathlib import Path
from tqdm import tqdm
import os
import glob
import pickle
# import logging
import numpy as np
import pa... |
ba9286d6fa52b37b88279d39da5eba62d3f6c462b9c10e41f3b6ae4518ba87c4 | Python | 108,705 | 3,189 | # -*- coding: utf-8 -*-
import threading, time, scipy, skimage
import numpy as np
import scipy.ndimage as ndi
# import tensorlayer as tl
from scipy import linalg
from scipy.ndimage.filters import gaussian_filter
from scipy.ndimage.interpolation import map_coordinates
from six.moves import range
from skimage import exp... |
a6258bcba9cf8449dddad956a519be30f4d874437c005b234670ab05cf800fbf | Python | 110,770 | 3,049 | __author__ = 'duarte'
"""
============================================================================================
Visualization Module
============================================================================================
(incomplete documentation)
Provides all the relevant classes, methods and functions fo... |
fe53c4d1bdf031f12deeede46e3990442f92ee3591baf013d31c3a42a6214121 | Python | 112,606 | 2,358 | #!/usr/bin/env python3
# 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>.
"""carla-pack: author, build, inspect, verify and install CARLA content packs.... |
389671cb71584a0f9d9e91b4af78cd9fe3f1439f54431d5454075af3e5c5e9a2 | Python | 113,611 | 3,065 | # cython: language_level=3
# Time-stamp: <2025-11-14 19:08:47 Tao Liu>
"""Module for filter duplicate tags from paired-end data
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------... |
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