sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
39efe3072992e958dfaaf9680110c13f9611e4fdb648984ab378ff21d62067bc | Python | 57,583 | 903 | #!/usr/bin/python
# -*- coding:utf-8 -*-
import logging
import os
import time
import warnings
import math
import torch
from torch import nn
from torch.utils.tensorboard import SummaryWriter
import numpy as np
import models
import datasets
from loss.DAN import DAN
from loss.JAN import JAN
from loss.CORAL import CORAL
... |
53d8f4c5933979070618ef9c40b6071fc26e340486f68411cf8ca0f69ebd50a6 | Python | 57,638 | 1,573 | # -*- coding: utf-8 -*-
# transformations.py
# Copyright (c) 2006, Christoph Gohlke
# Copyright (c) 2006-2009, The Regents of the University of California
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions a... |
479eeda3a1c8bd65664578ddc9bd7dd47c280b798e5ada569e9bb7e884e0fc8e | Python | 57,651 | 1,445 | """Functions for visualizing results
"""
import os, pickle, mne
import numpy as np
import pandas as pd
import seaborn as sns
import nibabel as nib
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
from matplotlib.colors import LinearSegmentedColormap, Normalize, CenteredNorm
... |
faf9705c851fef23f51784b60dfa718cdf3b2cd60b529df4439344347aedfc80 | Python | 57,677 | 1,363 | #!/usr/bin/python3
import tensorflow as tf
from abc import ABC, abstractmethod
from tensorflow.keras import layers as k_layers
from tensorflow.keras.layers import MaxPooling2D, Conv2D, Input, \
UpSampling2D, Concatenate, Dropout, ZeroPadding2D, \
GlobalAveragePooling2D, GlobalMaxPooling2D, Dense
from tensorfl... |
81c6a9d49056bd18bcb5636fd876fea0d976da5f0f3f72ff4edfc724cc40d2ed | Python | 57,852 | 1,651 | # isubplot
import os
import sys
from time import time
import numpy as np
import matplotlib as mpl
#'''
if mpl.get_backend() != 'Qt6Agg':
mpl.use('Qt6Agg')
import PyQt4.QtCore as QtCore
#'''
import matplotlib.pyplot as mp
import matplotlib.widgets as mw
from matplotlib.patches import Rectangle
from pyclamp.dsp.lsfu... |
9f24f103656b856dd06e43b0ab21e0af1bb0a6be2d1892ebe9bd5687b32d0b51 | Python | 57,932 | 1,183 | """Schema compliance checking for HED schemas.
This module is designed for HED 8.3+ schemas, which carry full domain and
range metadata on their attributes. It can be run on any loaded schema, but
schemas earlier than 8.3 will produce extensive known compliance errors
because they lack the attribute metadata that 8.3 ... |
b14c01925d1db91ca4412132d00acb6b3e2db4c195c07d1533b7a439086b4a16 | Python | 58,082 | 1,281 | """Parameters tab - advanced registration pipeline settings.
Contains:
- ParametersTab(QWidget): Laplacian solver, reproducibility, pipeline options,
and image preprocessing controls.
"""
from PySide6.QtWidgets import (
QVBoxLayout,
QHBoxLayout,
QGridLayout,
QWidget,
QLabel,
QCh... |
93785f4b952dd2eb495652aaabc582f3ab871c829c3bd23f25d0d2e7611d7fc1 | Python | 58,112 | 1,375 | import run_apt_expts_2 as rae
import os
os.environ['CUDA_VISIBLE_DEVICES'] ='0'
from importlib import reload
import APT_interface as apt
reload(apt)
import matplotlib
matplotlib.use('TkAgg')
from matplotlib import pyplot as plt
plt.ion()
import PoseTools as pt
import numpy as np
import cv2
from matplotlib.pyplot import... |
a38d90867114bb481c77a406ec8b41e8fd7a6e7102b1c34c3d2e66e4d42171e9 | Python | 58,147 | 1,426 | """
Unit and regression test for the pymochi package.
"""
import sys
from functools import lru_cache
import pandas as pd
import numpy as np
from pathlib import Path
from scipy import sparse as sp
import torch
import pytest
from loguru import logger
import pymochi.main as mochi_main
import pymochi.project as mochi_pr... |
c46866eeefbb307e37d969a44556512eeb3f67542fca97f56ae21557bc4d9d03 | Python | 58,175 | 1,247 | import sys
import skimage
import skimage.io
import skimage.measure
import skimage.morphology
import skimage.registration
import numpy as np
import pandas as pd
import os
import mrcfile
from scipy import ndimage
from scipy.spatial.distance import mahalanobis
from scipy import interpolate
from tqdm import tqdm
from . imp... |
a32ca16ba59dbae7eecd449065fd41faf5eb861d7aa0d66dee72112929fa1eea | Python | 58,199 | 1,308 | # coding=utf-8
# Copyright 2018 The Microsoft Research Asia LayoutLM 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/... |
0f07e8ecf5e05089f739612fa1b8fd2810d1a96f5f3bd383a290a39ea656977a | Python | 58,357 | 1,048 | """Continuous generation with a sliding token window and a persistent reservoir.
Working name: "Infinite Nekrasov". The language model sees at most `window` recent
tokens; the reservoir keeps evolving across the whole run.
Design decisions (see docs/CONTINUOUS_GENERATION.md):
- Prompt policy. "raw" (default): the se... |
2177aa952f5db1def711ea68da10baf41bf558cf8ecf1073f9448e0aab28a640 | Python | 58,387 | 1,056 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import time
import glob
import math
import seaborn as sns
from sklearn.decomposi... |
8dc7f5d35923dccc042cd455903b3058c733b35c3cff03676424cd4e79430e05 | Python | 58,401 | 1,364 | __author__ = "Zoe Wefers"
__credits__ = ["Ryan Huang"]
__version__ = "1.0.0"
__maintainer__ = "Zoe Wefers"
__email__ = "zoe.wefers@mail.mcgill.ca"
"""Purpose: Calculates four kinds of statistics about the localization of mRNA in dendrites/somas. For mRNA colocalization
and synaptic localization performs 100 simulatio... |
29f3ac361bc6ad8def05186e5cf00646734a44799a739e55153d876d80c73699 | Python | 58,427 | 842 | """Interpolate GKs to cube centres for MonoAlg3D simulations"""
import os
import sys
from warnings import warn
import math
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from datetime import datetime
import pymp, multiprocessing
if __name__ == '__main__':
anatomy_subject_name_list = [... |
b3a8130bd35da9414db3f2d0c058665011a2f9f072282238e094c168693597e9 | Python | 58,464 | 1,425 | import os
from os.path import join as pjoin
import nibabel as nib
import numpy as np
import pandas as pd
from fracridge import FracRidgeRegressor, fracridge
from joblib import Parallel, delayed
from nilearn.glm.first_level import FirstLevelModel, make_first_level_design_matrix
from nilearn.image import load_img, concat... |
2ba31ee5dadd5644da081372aa66a5b05bc160ea15f68d370cf081920faa4273 | Python | 58,491 | 1,602 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Collection of classes defining forward models applicable with current dipole
moment predictions.
Copyright (C) 2017 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public... |
afc3a69af34a0be725831b9bdaff1f1e2a4fa52c3c26c7814e62f4585e5e1c6a | Python | 58,569 | 1,282 | import unittest
from functools import partial
from hed.errors import ErrorContext, ErrorHandler
from hed.errors.error_types import DefinitionErrors, ValidationErrors
from hed.models.hed_string import HedString
from hed.schema.hed_schema_io import load_schema_version
from hed.validator import HedValidator
from hed.vali... |
1ea3947b1fa82ecca66cae4642ad9ab0cb199b8781167c76418c16161f0bca94 | Python | 58,590 | 1,519 | """
Module for importing and exporting 2p imaging datasets
(c) 2015 C. Schmidt-Hieber
GPLv3
"""
from __future__ import absolute_import
import os
import sys
import abc
import glob
import time
try:
import lzma
except ImportError:
import backports.lzma as lzma
if sys.version_info.major < 3:
try:
imp... |
265199b28ea68e5a2d059d56d5215acd7fa8853b3bb3fe141f08adbbabb5f922 | Python | 58,745 | 1,423 | # coding=utf-8
# Copyright 2019-present, Facebook, Inc 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
#
# Un... |
37607f9269fafebc0546ddf90461493e03156a82aecf9fed805a550a8c907cda | Python | 58,776 | 1,456 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team, Microsoft Corporation.
# 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 copy of the License ... |
aa6f3061044217538dbaf9191a758cd31df2106b8c63442ab0c3689a84490bb7 | Python | 58,839 | 1,671 | """
Holds classes for containing information for Gene and Fusion exon and protein information.
"""
import itertools
import os
import re
import sys
from Bio import Seq, SeqIO, SeqRecord, SeqUtils
from agfusion import exceptions, plot, utils
class _Gene:
"""
Stores the necessary information to specify the ar... |
5f7e1f2ec53f73790dd7967278eee01187395797da162da6d8fa77c46cc11b99 | Python | 58,845 | 1,059 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import time
import glob
import math
import seaborn as sns
from sklearn.decomposi... |
589e760ff5a0aefe35bd70283ce3cc7511792c5c0768d3e1805a7161fc09922e | Python | 58,984 | 1,193 | import os, sys
import numpy
import matplotlib
#matplotlib.use('tkagg') # For use on CSCS daint
from matplotlib import pyplot as plt
from matplotlib.gridspec import GridSpec
import matplotlib.animation as animation
import time
import argparse
import pickle
from scipy.signal import lfilter, resample
from scipy import io... |
bee9d80fdf01d04556f80377c2d63e5c74fe26602853fa50594a6d2757fb68f2 | Python | 59,021 | 1,519 | # -*- coding: utf-8 -*-
#
# Syncopy's main abstract base class + helpers
#
# Builtin/3rd party package imports
import getpass
import socket
import time
import sys
import os
from abc import ABC, abstractmethod
from hashlib import blake2b
from itertools import chain
from types import GeneratorType
import shutil
import n... |
5fe0485624273cb569f2160d0857ed287ca30a9c2e80fd3288643957a2670c63 | Python | 59,149 | 970 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'e:\project_wuqiyun\GUI_design\GUI_design_qiyun\PyTDL\PyTDL_GUI\PyTDL.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file ... |
c20b166a120e1caaadc1961c9afcc930c0aa48f24de023be62d5e2ed8aedfc8c | Python | 59,183 | 1,524 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
c2da365d4a344d4eb89b58d907f91867275e93cc8474219522d4ec97a468b245 | Python | 59,227 | 1,391 | import os
import sys
import pdb
import glob
import json
import pickle
import itertools
import functools
import multiprocessing
import scipy.stats
import numpy as np
import pandas as pd
import util
def load_eval_dict(fn_eval, keys_to_ignore=[]):
"""
"""
with open(fn_eval, 'r') as f_eval:
eval_dict... |
1c98be56f71f4c485f3d3f47b8b26fb678c2bc7ffb41b125719c98298d6b934e | Python | 59,271 | 1,801 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Class methods defining multicompartment neuron populations in the hybrid scheme
"""
import os
# import glob
import numpy as np
import h5py
import matplotlib.pyplot as plt
from mpi4py import MPI
# from .gdf import GDF
from . import helpers
from .helperfun import _calc_ra... |
b57a49142ead94f3f0e2a78fd6288e7d70446f6ce7f15b7823f34a1ccd9ff58b | Python | 59,408 | 1,308 | # Copyright (c) MONAI Consortium
# 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, so... |
db098516905d5e521c0903567e48ac7a28eb245c61f0a3f64b9a6317dd5665c1 | Python | 59,452 | 1,117 | import time
import math
import os, shutil
import numpy as np
from unittest import TestCase
from ..model import ModelCSRV, ModelSRPV, Model2CCSRV, gen_tlist, gen_tlist2
from ..utils import iso_surface, poly_decimate, disperse_io, stat_dict_to_mat
from ..surface import Particle, TomoParticles, ListTomoParticles
from matp... |
97a00786580d41c552c82870feac53570a2c4e50ab3da2daeae1f3bf9f3c321d | Python | 59,489 | 1,630 | from dreamcoder.program import *
from dreamcoder.type import arrow, baseType, tint, tlist, t0, t1, t2, tboolean
from dreamcoder.task import Task
from dreamcoder.grammar import Grammar
from dreamcoder.program import Primitive
#from dreamcoder.domains.arc.arcPixelwisePrimitives import _stack_xor, _stack_and, _apply_funct... |
59fb9eae1d53284a379c20d8769ff5516425925092359c3b6c9073ea0a249a3f | Python | 59,577 | 1,015 | # Tensorflow implementation of the Lagrange model. Trainable only with single samples.
#
# Authors: Dominik Dold (dodo47@github) and Benjamin Ellenberger (benelot@github)
import numpy as np
import time
import tensorflow as tf
import tensorflow.nn as nn
from tensorflow.python.client import timeline
# network paramete... |
e4ac242c67d15631e013a6d121a3a2b9be8c3f290da1d0a60d569177a2b668ce | Python | 59,674 | 1,577 | import os
import sys
import webbrowser
import time
import numpy as np
import scipy as sp
import scipy.stats as stats
import numpy as np
import scipy as sp
import scipy.stats as stats
from pyclamp.dsp.lsfunc import *
from pyclamp.dsp.fpfunc import *
from pyclamp.dsp.iofunc import *
from pyclamp.qnp.bqa_dgei import BQA
... |
d4917fa99730c1d6d071fb66f9afefe537f43a44a382bbc9d86e71f97bc803e6 | Python | 59,697 | 1,426 | # coding=utf-8
# Copyright 2019 The Google AI Language 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/LICEN... |
9f8285f6f932f3fe6261e5dcc993c4bf3c8ba655a50ef14b90ce4923406cd3c0 | Python | 59,706 | 1,702 | import io
import sys
import typing
import warnings
from abc import ABC, abstractmethod
from collections import deque
from dataclasses import dataclass, field
from datetime import timedelta
from io import RawIOBase, UnsupportedOperation
from math import ceil
from mmap import mmap
from operator import length_hint
from os... |
98d6173bcb896e9f2e29311b4f4e3629f18165eeb9cd06cbeeebcdd861cf1447 | Python | 59,736 | 1,114 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
28f5e3813432fa6280193924446620592250616c8fae501f0ff07e3e153a549e | Python | 59,839 | 1,304 | # coding=utf-8
# Copyright 2021 The Fairseq Authors and The HuggingFace Inc. team. 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/... |
db9f855e5c49d0f43bf627f07e1e53bada4fdaad5eb50cbfae1b71d8b54e4043 | Python | 59,900 | 1,645 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 you... |
727ea8102bed150de393cdd910e5cef8f8777f3889bcbbf12b0292240bb21306 | Python | 59,974 | 1,494 | #!/usr/bin/env python3
#******************************************
#
# SHARC Program Suite
#
# SHARC-MN Extension
#
# Copyright (c) 2023 University of Vienna
# Copyright (c) 2022 University of Minnesota
#
# This file is part of SHARC-MN.
#
# SHARC is free software: you can redistribute i... |
7204a11aa5a000876f4b235a201e78361872d06ed01020bb8676cfc6f625dfa7 | Python | 60,123 | 1,727 | """
Visualization of histograms summarizing the distributions of
burst characteristics within a burst dictionary.
Visualization of a random subset of burst waveforms and their
average.
Visualization of the components generated by the dimensionality
reduction step.
"""
import numpy as np
import matplotlib.pyplot as p... |
158fb751221c2e1cbbf3fd79431cac06c50ce09e96acb91027f8bea21549bb37 | Python | 60,177 | 1,650 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 you... |
a99c478789d05bd41b6ed62313a36a6d4098ba1c48fc664e4c519bf10d339445 | Python | 60,313 | 1,655 | import random
from typing import Any
import bpy
import MDAnalysis as mda
import numpy as np
import pytest
from databpy.nodes import get_input, get_output
from MDAnalysis.tests.datafiles import DCD, GRO, PSF, XTC
from nodebpy.nodes.geometry import (
Compare,
GetBundleItem,
GetGeometryBundle,
Group,
I... |
225ce725930b5d29c3f6239c0684e4a3905266e44d19fbd44170864ee98b2f5e | Python | 60,315 | 1,520 | """
Contains class SegmentationAnalysis
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import division
from builtins import zip
#from builtins import str
from builtins import range
from builtins import object
#from past.utils import old... |
92272bf61abe2f384bf2eaf99bd05ef6d2cb81a04e7a09e631c98ea6bfd3703d | Python | 60,324 | 1,812 | import PoseTools as pt
import numpy as np
import TrkFile
# 10 zebrafish
id_file = '//groups/branson/home/kabram/Downloads/idstuff/10_fish_group6/first/iddat.pkl'
mov_file = '/groups/branson/home/kabram/Downloads/idstuff/10_zebrafish/group_3/TU20171214_N10_Group6_first_01-18-18_17-35-02.avi'
# mov_file = '/home/kabram/... |
c13408a78f223fd41eff5080ccdcd28428d0ae48ad11e672f8484a5d2c12166c | Python | 60,340 | 1,814 | # Copyright (c) 2020, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and t... |
9f4c1fe3521808aff900902f3ee2206de6883674dbb52921728116ad5c70aaa9 | Python | 60,675 | 1,078 | # set QT_API environment variable
import os
import sys
import time
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
from control._def import *
# app specific libraries
import control.widgets as widgets
import serial
if CAMERA_T... |
cb7e3f183d624cf1dba2936a489a4807fd71b079b66836f91016426c0a3ada2c | Python | 60,764 | 1,939 | """Contains functions and classes for handling entries within objects.
CLASSES
-------
FillerObject
- Empty object that can be filled with attributes that would otherwise not be
accessible as a class attribute.
FUNCTIONS
---------
check_lengths_dict_identical
- Checks whether the lengths of entries within a d... |
bc729d7f16795fea91142d6771fd44c8ce821e2877e5704d8092603ae5f5e427 | Python | 60,806 | 1,395 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles densities by list
... |
39b5b8f704cbe79d2982e98db2b1111d0cf85c3cd1ed786b6bbfe35ecc28f1b2 | Python | 60,880 | 1,489 | # coding=utf-8
# Copyright 2026 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... |
bc67d05940ee5311fe48b9a9f03b05a5d0813852208bc821c21aa5d718357853 | Python | 61,002 | 1,522 | from PoseCommon_dataset import PoseCommon, PoseCommonMulti, PoseCommonRNN, PoseCommonTime, conv_relu3, conv_shortcut
import PoseTools
import tensorflow
vv = [int(v) for v in tensorflow.__version__.split('.')]
if (vv[0]==1 and vv[1]>12) or vv[0]==2:
tf = tensorflow.compat.v1
else:
tf = tensorflow
import os
impor... |
afb69ea228b1c718a70292ea47fd188b4485320bb6d15133d4e1d4af494d4ba7 | Python | 61,007 | 1,582 | from __future__ import print_function
from builtins import zip
from builtins import str
from builtins import chr
from builtins import range
import scipy.io as sio
import os
import sys
import myutils
import re
import numpy as np
import cv2
from cvc import cvc
import math
from random import randint, sample
import pickle
... |
fb6ac3f17becbd43761315949ce806b39ef1cc70a1390a757a16dcee2928d03e | Python | 61,171 | 1,400 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles densities by list
... |
1ef59a9b89fc1ed29b2abf4569b4ea0007218b2c35392b5e77c80ebd6d5cae34 | Python | 61,179 | 1,400 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles densities by list
... |
65d570027a83edababf97258193f24ada8325b723290de49e45e68d0f6417a48 | Python | 61,225 | 1,401 | """Registration GUI dialogs.
Contains:
- Preview2DDialog: side-by-side 2D input vs CCF template with flip/rotate controls
- RegistrationResultDialog: post-registration viewer with lazy loading, LRU cache, annotation overlay
- ManualSetupDialog: fallback manual component selector for non-standard output directorie... |
163b6eba3a273272c55af675e2e53be8a8325b82ba2fd511e6952b1a964156ec | Python | 61,307 | 1,749 | __author__ = 'martinez'
import math
import shutil
from .variables import *
import scipy as sp
import random as rnd
from pyorg import pexceptions
try:
import pickle as pickle
except:
import pickle
###### Global analysis
# Unpickle a Generic PySeg object
def unpickle_obj(fname):
# Load pickable state
... |
f3d95676e8d2b72d005da1b17565ebd556cadc941864744ad8558e2773f10348 | Python | 61,674 | 1,521 | # coding=utf-8
# Copyright 2020 Microsoft and the Hugging Face 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
#
# Unless require... |
b903015e60482a8e58b3847809b43d88e8f23e73f06ecafb357b2a3a8befd998 | Python | 61,697 | 1,832 | # coding=utf-8
# Copyright 2026 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... |
b3f10150849b39ce7ce185b3f56cac6c29cf56cb4bbadbdf987388b89e523cfc | Python | 61,711 | 1,405 | import pandas as pd
import seaborn as sns
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from vedo import *
import colorcet
def join_model_results():
"""
Auxiliary method to join pandas dataframes containing cvrmse results for different ML model... |
7039925c3d763ae2c57e82da143725aa78d4ff10dac1d8bf24be5b6b5f958648 | Python | 61,734 | 1,676 | # Copyright 2020 The HuggingFace Team, the AllenNLP library authors. 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
#
... |
d4b826e96221da787612d3109f8bf8def91155bcf6dfca04b594e7e734ababeb | Python | 61,769 | 1,727 | import numpy as np
import warnings
from pyclamp.dsp.lsfunc import *
from pyclamp.dsp.dtypes import *
from pyclamp.dsp.cstats import *
from pyclamp.dsp.sifunc import *
#from numpy.core.umath_tests import inner1d
from numpy import dot as inner1d
import scipy.signal as signal
import scipy.special as special
import scipy.s... |
47a9b8721d65ffceea337070c5ae5fc17ad072884df3d72bb93f50b3134ef3cb | Python | 61,791 | 1,518 | # coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. 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 r... |
1bd662b4b039b4eb52c49a748570a7062f64de973283df244c3e85353caf825c | Python | 61,802 | 1,658 | """
Contains class ImageIO for image file read/write.
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins imp... |
ab744d63a37b40f0b5f196c0988a585e8aa06c101dbccfbcf837d7aae4523dbc | Python | 62,042 | 1,494 | #!/usr/bin/env python
# Copyright (c) 2019 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 CARLA No... |
d4c99253a04c34158c362793f52f3c4e67f0bff9813eee5ed548f6dcd6296b1f | Python | 62,158 | 1,316 | # MEGIT overview preprocess GUI
import os
import copy
import json
import h5py as h5
import math
import numpy as np
import cv2 as cv
from ..data import get_frm, brt_con, draw_text
from ..utils import mk_outdir
from PySide6 import QtCore, QtGui, QtWidgets
from .dgn_preproco_ctrl import Ui_ControlViewer
from... |
76c5c83f21bf8e91a44579033a7488e2d9de07fe760948c99c7b9fe799b2a535 | Python | 62,345 | 1,614 | import datetime
import json
import os
import keras
import numpy as np
import pandas as pd
import scipy
import tensorflow as tf
import tensorflow.keras as keras # # important to make sure non tf.keras is hidden
from scipy.stats import *
from sklearn.metrics import *
from sklearn.model_selection import train_test_split... |
e9691329a2e9a13ecb9ce551b2e54a64f62feae59bbbe392cdd0ab10a611aa8c | Python | 62,362 | 1,711 | from __future__ import division
from __future__ import absolute_import
import pandas as pd
import numpy as np
# from sympy import N
import h5py
import os
from pathlib import Path
from .detection_localisation.detect import detectData
from .detection_lightning.detect import HSDetectionLightning as detectDataLightning
fr... |
5b9f04375d78c8142da6415ddee5bf57abe3afee03c85015508d78571839a6bd | Python | 62,410 | 1,467 | import os
import json
import shutil
import pandas
import numpy as np
import tifffile
import importlib
import time
import logging
import pickle
import datetime
import networkx as nx
import collections
from matplotlib import pyplot as plt
from typing import List
from typing import Tuple
from typing import Union
from typi... |
1b94b3862eeaffe71521e27e0b93adffa57bcd667647f5d5f0f848c657c3f11f | Python | 62,458 | 1,332 | """
ANTs SyN registration functions.
Provides registration, transformation, deformation field export,
and point transformation using ANTsPy.
"""
import os
import sys
import gc
import shutil
import tempfile
import numpy as np
from regtools.utils.io.volume_io import save_atomic
from regtools.utils.loggi... |
0ee914f5df5d56ea7184fc7e0b5da8bd7f415fad7727784d053e147dc51287f7 | Python | 62,503 | 1,357 | # coding=utf-8
# Copyright 2021 The Fairseq Authors and The HuggingFace Inc. team. 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/... |
0bbc7608fa7fd81cbe09b6f4099dd0f5d8f739f178643dd313244e21728a4f5b | Python | 62,539 | 868 | import torch
from torch.nn import functional as F
from torch_scatter import scatter_sum, scatter_mean, scatter_add
from torchdrug import core, tasks, layers, models, metrics, data
from torchdrug.data import constant
from torchdrug.layers import functional
from torchdrug.core import Registry as R
from torchdrug.models ... |
566e4eb0782c569124c9359299a201c2aa308483f87679bf668cdab4dfdab078 | Python | 62,680 | 1,206 | import os
import unittest
from hed import schema
from hed.errors.error_reporter import ErrorHandler
from hed.errors.error_types import ErrorSeverity
from hed.schema.hed_schema_constants import HedKey, HedSectionKey
from hed.schema.schema_validation.compliance import (
CONTENT_SECTIONS,
DOMAIN_TO_SECTION,
S... |
b9f92be682667389b40b1e64ae07eaf2cf44db80d10c960e82e5327edaefc9e6 | Python | 62,786 | 1,268 | """
Confidence-driven incremental active-learning experiment, generalized across
datasets.
Idea: train on a small labeled subset, then repeat: run the latest
checkpoint over the full candidate pool, rank pool images by the model's own
lowest predicted per-keypoint confidence (images where it missed an animal
entirely ... |
db0ab942081c3ddc54c2e52b5ada460102bda265637c8d3087d3995fbf6a4e16 | Python | 62,925 | 1,736 | #!/usr/bin/env python
#
# Copyright 2007 Neal Norwitz
# Portions Copyright 2007 Google Inc.
#
# 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... |
ab60cfccd79058d27b761d95314d9172b62e4e474b733607c4c5787484f7ff8d | Python | 62,931 | 1,474 | """
Functions to create meshes for demos.
:func:`create_cubes` defines a 'cube-in-a-cube' mesh using the
built in :class:`dolfin.UnitCubeMesh()`, with subdomains defined and
marked by :func:`facet_topology` and :func:`cube_condition`
:func:`create_spheres`, :func:`create_ellipsoids`,
:func:`create_cylinders`, and :fun... |
330c092d5cfedd1d3760f5d6786c985905f106c44a3bc3868a78342f233e2688 | Python | 63,217 | 1,324 | """
Creates graphs for task re-ranking metrics from an ECResults checkpoint.
Requires metrics to be available in a recognitionTaskMetrics dict: you can specify this via --storeTaskMetrics.
Or you can attempt to back add them using the --addTaskMetrics function.
Usage: Example script is in taskRankGraphs.
Note: this r... |
15a51f1b5e0d04910a2d0a18f6a8fa258797ae961c2e62ae96085dc4e18568e7 | Python | 63,223 | 153 | """
pygments.unistring
~~~~~~~~~~~~~~~~~~
Strings of all Unicode characters of a certain category.
Used for matching in Unicode-aware languages. Run to regenerate.
Inspired by chartypes_create.py from the MoinMoin project.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
... |
4ce0d294b167405f4c4d1b3aa63f77582ffbae4d580c2626077ff92419494289 | Python | 63,264 | 1,530 | from datetime import datetime
import functools
import glob
from gudhi.clustering.tomato import Tomato
import h5py
import matplotlib
from matplotlib import animation, cm, transforms, pyplot as plt
from matplotlib.collections import PathCollection
import numba
import numpy as np
from ripser import Rips, ripser... |
581718ac785c7b5122317bb424bbb817a1fbf178963ba98df7accf06b638d876 | Python | 63,298 | 1,894 | # coding=utf-8
# Copyright 2026 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... |
56b6e57d0ba331beb859d3677f3a379a3bfb04a54b5df9cfb8f7e470f1dbdd02 | Python | 63,507 | 1,783 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
d06ab779a9edc035a639f9e327a7b15ad20befe635846f0b4e8d3759caae4b86 | Python | 63,849 | 1,429 |
"""
MoCHI project module
"""
from loguru import logger
import itertools
import os
import pickle
import shutil
import torch
import pathlib
import numpy as np
import copy
from scipy import sparse as sp
from pathlib import Path
from pymochi.data import *
from pymochi.models import *
from pymochi.report import *
class M... |
d7ea9fcc6f378c8ebe65a75076b69e63c0337856bd896fa62d3aff7cd2b75038 | Python | 64,011 | 1,462 | #!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import glob
import io
import collections
import pickle
import pandas as pd
import numpy as np
import seaborn ... |
087212ccc3b6e119616f1b7012e338ed487d80e8892fadf8dea972f8c12b8857 | Python | 64,107 | 1,499 | # 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... |
ac6e01a3a1f9a5808187ab03cbc69882c69871bd500bd914a4dfa804761f72da | Python | 64,190 | 1,726 |
import sys
import struct, collections
import warnings
import os.path, hashlib
import os, stat
import numpy
import numpy as np
from numpy import nan
import logging
import time
import math
import FlyMovieFormat as FMF
def bchr(intval):
return bytes(bytearray((intval,)))
class UfmfError(Exception):
pass
cl... |
19f7912bb39df56169625e0e4cf105caa8cadcbfa8e8355f3ea29c1a117806e5 | Python | 64,229 | 1,967 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Plotting function helper script
'''
from matplotlib.colors import LogNorm # , SymLogNorm
from mpi4py import MPI
import analysis_params
import plotting_helpers as phlp
import neuron
import LFPy
from hybridLFPy import helpers
import h5py
import glob
from mpl_toolkits.axe... |
073372d5b2c498ab7e52a744ef0f8ef9df9a4684409a7fe71e552e5f497c19f7 | Python | 64,260 | 1,438 | # coding=utf-8
# Copyright 2018 Hao Tan, Mohit Bansal, and the HuggingFace 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
#
# Unless r... |
b99e9e61c1eafc7cf1c3a3e1d7e527704072c7b1d320b49a5d69ae99fdd21487 | Python | 64,487 | 1,414 | from __future__ import annotations
import random
import time
import warnings
from collections import defaultdict
from functools import partial
from math import floor, nan
from typing import TYPE_CHECKING, Any, Literal, cast
import anndata as ad
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
im... |
e47af59321d64cbc157c99bad6cfeb001673c4e79599f7d3d002d5be49c5995e | Python | 64,549 | 1,549 | # 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... |
9c1708a4b54248f1c9ed8e9816b02dc691005d06b704cf1e89794a15aef24961 | Python | 64,592 | 1,679 | #!/usr/bin/env python
"""
Functions used to display analysys results for presynaptic_stats.py script.
This was previously part of presynaptic_stats.py.
Work in progress (03.2018)
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import p... |
22818a5c8d3216fd2965fe817ecaadbd65f413ef3239b127f424724d078c54b7 | Python | 64,629 | 1,565 | # MIT License
#
# Copyright (c) 2020 The Google AI Language Team Authors, The HuggingFace Inc. team and github/lonePatient
#
# 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 restricti... |
9d2fc18f13b97cdf57c85bda2a3c2eb8b5277437d37155a3de2220abdc941e65 | Python | 64,716 | 1,430 | from pathlib import Path
import time
import numpy as np
import openturns as ot
ot.Log.Show(ot.Log.NONE)
from uptake.figures.utils import CreateFigure, Fonts, SaveFigure, XTickLabels, XTicks
import uptake.metamodel_implementation.utils as miu
class DataPreSetting:
"""A class that performs the presets on ... |
977dcdeea42081468170e25223d847b17eaeff3b47941ec41836d35be6167bf7 | Python | 64,824 | 1,747 | """Classes for parameters, species, compartments, reactions, fluxes, and forms.
Model class contains functions to efficiently solve a system.
"""
import dataclasses
import logging
import numbers
import sys
from collections import OrderedDict as odict
from dataclasses import dataclass
from enum import Enum
from pprint i... |
b5ae893ef49676c225dfef0b2ea6134d7eedbc818b2aa8bdf59f07fa71f3aee4 | Python | 64,830 | 1,227 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.colors
import pickle
import dill
import os
import glob
import math
import re
import seaborn as sns... |
b2803e13253f4a97399948802940c2166ab1fdcf3d012dc7dd3b9069ca00986c | Python | 64,976 | 1,520 | import itertools
import os
import pickle
import tempfile
from types import SimpleNamespace
import bpy
import databpy
import MDAnalysis as mda
import numpy as np
import pytest
from nodebpy.nodes.geometry import SetPosition
from numpy.testing import assert_almost_equal
import molecularnodes as mn
from molecularnodes.node... |
1021e8b6b172e8ba94fe59c82a7b042039e3750c0dfb0e3076615f81e6c2b8d9 | Python | 65,036 | 1,190 | import os
import json
import datetime
import pathlib
import time
import statistics
from collections import deque, defaultdict
import math
import numpy as np
import carla
from srunner.scenariomanager.carla_data_provider import CarlaDataProvider
from leaderboard.autoagents import autonomous_agent, autonomous_agent_loca... |
da427d53c40111e685b2090a78dc4c090e0eaeda1938e8963d4a4056be7695e6 | Python | 65,042 | 1,600 | from pathlib import Path
import scanpy as sc
from anndata import AnnData
from mudata import MuData
from scanpy import settings
from pertpy.data._dataloader import _download
def burczynski_crohn() -> AnnData: # pragma: no cover
"""Bulk data with conditions ulcerative colitis (UC) and Crohn's disease (CD).
... |
9eb55e432367315f68774c307c8a79be314b96ff13c7876d9351c51831ec04e2 | Python | 65,044 | 1,149 | # This file contains the ECG computation class
# And all the methods for ECG computation that can be considered
import multiprocessing
from abc import ABC
import numpy as np
import pymp
from scipy import signal
import matplotlib.pyplot as plt
from warnings import warn
from postprocess_functions import plot_histogram,... |
2aa5e9afdc9c634c0f55aaba3994b4254e219e3db749e336cef3c1e86c055409 | Python | 65,057 | 1,036 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from .scVI_distribution import *
from .utils import *
from .loss import *
import os
import copy
import random
import gc
import numpy as np
import pandas as pd
import scipy
import torch
from torch import nn, opt... |
177eb8313502681ae7c9e99feace888ddddeb31807f1b39d0ba6f53ba6a5f356 | Python | 65,470 | 1,522 | """
#!/usr/bin/env python
# -*- coding: utf-8 -*-
Code by Atchuth Naveen
Updated and maintained by Andy Thai
Code developed at UC Irvine.
Corrects deformation in individual images and stitches them into a large mosaic section.
"""
# Standard library imports
import sys
import argparse
import os
import gc... |
f9b9c59e9c1bc5247e64337d0ca825266b5a3ae5b2f9b96c57a0f8a0e8409455 | Python | 65,694 | 1,230 | from best_cut_node import best_cut_node
import numpy as np
from sklearn import datasets
from sklearn.neighbors import KDTree, NearestNeighbors
from sklearn.decomposition import PCA
import pandas as pd
from numpy.linalg import svd
from sklearn.preprocessing import StandardScaler, normalize
from sklearn.model_selection i... |
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