sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0b620d16e4dcc212e2fcff151856539ec88cffbdbd4259c69fbeb00a95e9173b | Python | 51,001 | 1,214 | """Registration quality metrics.
Provides pairwise image similarity and overlap metrics used to evaluate
registration quality. All functions accept 2D or 3D numpy arrays and
return a single float scalar.
Metrics
-------
getMutualInformation : Mattes mutual information (via SimpleITK)
getNormalizedMu... |
01cff2ec7873e1bae537dc11a2a497fa5327dcf73c6d526301e76c26c3696760 | Python | 51,017 | 1,206 | 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
from matplotlib import pyplot as plt
from typing import List
from typing import Tuple
from typing import Union
from typing import Dict
from... |
43269784f03b76760f7cfefc6d8a44321881db7142be0756f293016e4d5778da | Python | 51,028 | 1,146 | """ Module for comparing whisker activity across datasets: load whisker
data from all selected recordings (now 25 after filtering for no/bad
whisking) - using get_wskvar and prepare_df; analyse slope of avg
whisking behaviour (pre and post drop) within t_slope (inspired by
Variance_pre_post_betweenr.svg window where va... |
6faf1452a11e80e79c3d78c975384e25a9028f8d4056711265d2d427a97bd3d0 | Python | 51,035 | 1,396 | #============================================================
#
# Deep Learning BLW Filtering
# Deep Learning models
#
# author: Francisco Perdigon Romero, Wesley Chorney, and Ahmed Shaheen
# email: ahmed.shaheen@oulu.fi
# github id: AhmedAShaheen
#
#===========================================================
imp... |
0d813159a3cb4ea284e8a239f2bea36b30e171dc0825f8024e5aeaf713161a58 | Python | 51,051 | 995 | """A local neural observatory; all model work belongs to one dedicated thread."""
from __future__ import annotations
import html
import hashlib
import json
import threading
import time
from collections import deque
from dataclasses import fields, replace
from datetime import datetime
from pathlib import Path
import n... |
6f711ce76ec55ac10717617a761fb39b5c12a1a5fb01790ac3f13a6cb6e0e199 | Python | 51,083 | 1,387 | #!/usr/bin/env python
#
# 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
#
# Unless required by applicable law o... |
99ee7c256baa9347a4d0fc5313fb20bf1bc416adfb00b9d01a9a2a4015479b4c | Python | 51,084 | 1,387 | #!/usr/bin/env python
#
# 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
#
# Unless required by applicable law o... |
5106c60e2c69971735b209e824504e2f03511b376015c721b048cb6d48935450 | Python | 51,100 | 978 | import os
import json
from ckg.graphdb_builder import builder_utils
from ckg import ckg_utils
from ckg.analytics_core.analytics import analytics
from ckg.analytics_core.viz import viz
import pandas as pd
import itertools
import time
ckg_config = ckg_utils.read_ckg_config()
log_config = ckg_config['analytics_factory_lo... |
a47aa066cbc84fa9a2360270405a1e0add5ea423c4d073de9404938d42ee8846 | Python | 51,146 | 1,317 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from plot_methods import plotting_correlation, network_sketch, plot_population, plot_signal_sum, calc_signal_power, plot_population
from cellsim16popsParams_modified_spontan import multicompartment_params
import analysis_params
import plotting_helpers as phlp
from hybridLFP... |
adea7cd3d6884f3b2f4d44c2bb87c719f246119af542183c36eacd4fa00b8ce5 | Python | 51,193 | 553 | # TODO: maybe some OpenRAVE links are disabled
# http://openrave.org/docs/0.8.2/collada_robot_extensions/
# < extra
# type = "collision" >
# < technique
# profile = "OpenRAVE"
# ignore_link_pair
NEVER_COLLISIONS = [('base_bellow_link', 'base_footprint'), ('base_bellow_link', 'bl_caster_l_wheel_link'),
... |
7b9a80c481aa92753b55dc1b3321fb0d59dc6881014fcc01add8a5fbde077562 | Python | 51,219 | 1,364 | """
The Mapper generates a mapping between all the datasets involved by turning
all known type labels and synonyms into a graph and then trying to find
the minimal connected components of the graph.
The rule is this:
- for each neuron find *a* shortest path to a neuron in the other datasets (if it exists)
- keep only ... |
195ed2771c6ab258826539d9721cb1a5d10bc3b7e68ab00f140b4afef330dccb | Python | 51,229 | 1,231 | # -*- coding: utf-8 -*-
#
# Base class for all computational classes in Syncopy
#
# Builtin/3rd party package imports
import os
import sys
import psutil
import h5py
import numpy as np
from itertools import chain
from abc import ABC, abstractmethod
from copy import copy
from tqdm.auto import tqdm
if sys.platform == "w... |
0768be1d7a96b11317479ebe37ffd4065bfed80b329d5a9e675c4e76af07c51a | Python | 51,463 | 1,729 | from __future__ import annotations
import os
from copy import deepcopy
from io import StringIO
from logging import INFO, WARNING, getLogger
from pathlib import Path
from shutil import which
from types import SimpleNamespace
import numpy as np
import pytest
from ase.atoms import Atoms
from ase.build import bulk
from a... |
af943ce0eeb3d66113cebb0a71636fb3c4a8a86474e66cf234c39a66a8971112 | Python | 51,513 | 1,233 | """
Unit tests for the registration module.
Tests are organized into tiers:
- TestPureComputation: Pure math functions (no I/O, no external tools)
- TestImageUtilities: Functions that process numpy arrays (need numpy/scipy)
- TestNiftiIO: Functions that read/write NIfTI files (need nibabe... |
a3f9b0d1f02bf773430071c77ea1b9e18d478bd4647eba76057d795d66582b9d | Python | 51,697 | 1,350 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012-2017 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""PEP 376 implementation."""
from __future__ import unicode_literals
import base64
import codecs
import contextlib
import hashlib
import logging
import os
import posixpath
import sys
import z... |
e7968bd8c5f81b7d8c843819d1e2c7526cf90a5854bf2839b8dcc5965900db01 | Python | 51,735 | 1,560 | import os
import random
import time
import numpy as np
import pandas as pd
import torch
import torchvision
from torchvision.transforms import v2
torch.set_num_threads(1)
torch.set_num_interop_threads(1)
torch.use_deterministic_algorithms(True)
if torch.cuda.is_available():
torch.set_default_device("cuda:0")
... |
e1a6fd1abdc6e65480203d2840c238d33c16dbc7475b5d7bfa1cf929ed61623b | Python | 51,799 | 864 | import copy
import os
import json
import logging
import warnings
import torch
from tqdm import tqdm
import pandas as pd
import numpy as np
from torchdrug import data, utils
from torchdrug.core import Registry as R
from torch.utils import data as torch_data
from cg_steps_energy_injection import cg_protei... |
c0dcc6fb3111cd2fd71a5b3e9c13d55722d11dadac9149649f4fb99f4b6b3160 | Python | 51,991 | 1,300 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012-2015 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
import gzip
from io import BytesIO
import json
import logging
import os
import posixpath
import re
try:
import threading
except Impo... |
31de2168dbc7935291cd49affbdbfdc31f14eae91ebd4c3431e5255e5e87a477 | Python | 52,166 | 1,271 | # 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... |
f0725bc343f5d28b92d670d3dd5d65f283a23a6a337ce473bbfd85bc292d09f0 | Python | 52,189 | 1,561 | from random import Random
from fitnessFunctions import fF,frange
import sys
import logging
from numpy import random
import numpy as np
import copy
import array as array1
import random
import json
import time
import os
import bluepyopt as bpop
import bluepyopt.ephys as ephys
from math import sqrt
import inspyred
from in... |
6c612f9fba107e0b53f39023a2336e0a5742a38962a93bd580950808a7551e91 | Python | 52,265 | 1,282 | from math import fsum, sqrt
from copy import copy
from pyelectro import analysis
from traceHandler import sizeError
import efel
import numpy as np
import scipy
import inspyred
from inspyred import ec
from inspyred.ec import emo
from inspyred.ec import variators
from inspyred.ec import observers
import modelHandler
impo... |
a867400f895bd163b7e4c86d7a508b762a4642ea5e66a465895be0a7ef3f5cf8 | Python | 52,286 | 1,036 | ################################################################################
# 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... |
a9595414df03c347d466f4dd2d1e12b4616f62b0d37995a2c81a68ae89b13a3a | Python | 52,291 | 1,071 | import pandas as pd
import numpy as np
from sklearn.metrics import silhouette_score
from matplotlib import pyplot as plt
from os.path import exists
import random
from math import ceil
import matplotlib
import time_series_tools as ts_tools
#------------------------------
# Clustering-related functions:
#--------------... |
5ce0848e8638e04ec3f3791e6a206f6f5aa799eeb91deb91d56d33849674999b | Python | 52,398 | 1,248 | # coding=utf-8
# Copyright 2019-present, the HuggingFace Inc. team, The Google AI Language Team and Facebook, 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.or... |
03fd0426b46c9aba713d3e33201a41e608374773a5ce16acfc12ebf530bc6bc1 | Python | 52,629 | 1,253 | """
GUI for converting images and points to Neuroglancer format.
"""
import os
import sys
import glob
import traceback
from natsort import natsorted
from PySide6.QtWidgets import (
QWidget,
QVBoxLayout,
QHBoxLayout,
QLabel,
QFileDialog,
QCheckBox,
QPushButton,
QDouble... |
7cdaa4744fbbec32b1c226eef9b72877d0e0f467c3e04b4e7144078290c97496 | Python | 52,693 | 1,093 | #!/usr/local/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import copy
import scipy
import logging
import operator
import collections
import yaml
import numpy a... |
f4309cb34756fabefb0b5a9bd15c3b5f2fd7ec790052e40baa33b5a5e9900b23 | Python | 52,793 | 2,334 | from __future__ import annotations
from dataclasses import dataclass
from joblib import (
Parallel,
delayed,
parallel_backend,
)
import numpy as np
import pandas as pd
from threadpoolctl import (
threadpool_limits,
)
from sklearn.metrics import adjusted_rand_score
from sklearn.mixture import Gaussi... |
8fa57aaeee113f5d12abfee522465975c64959a01c943d70a624ef04338d4841 | Python | 52,859 | 789 | """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
# def convert_from_monoalg3D_to_cm_and_translate(nodesXYZ, meshname):
# warn('Hi ... |
f9228ab63a8951d7a1d3480a8243247d031a3593504f4f1390d8367f3d207a60 | Python | 52,906 | 1,341 | from dreamcoder.grammar import *
epsilon = 0.001
def instantiate(context, environment, tp):
bindings = {}
context, tp = tp.instantiate(context, bindings)
newEnvironment = {}
for i,ti in environment.items():
context,newEnvironment[i] = ti.instantiate(context, bindings)
return context, newE... |
b70cc8959e1e7a8ac0bcfd552e7720e4cfcb6d440b826c50db88823d7e976222 | Python | 52,908 | 761 | """This script visualises the results from the inference of repolarisation properties from the T wave"""
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
if __name__ == '__main__':
if len(sys.argv) ... |
03f25605dd3627c960f77a3a5618249c1188d54660feb4e27c89e779c2d3fa5b | Python | 52,958 | 763 | """This script visualises the results from the inference of repolarisation properties from the T wave"""
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
if __name__ == '__main__':
if len(sys.argv) ... |
4c52c3e5b9cb2609a1ce74ec6eea78967e5509d354156fab10d79643e4e6d701 | Python | 52,974 | 1,528 | """
Contains class Affine for preforming affine transformation (general linear
transformation followed by translation) on points (vectors).
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import div... |
b27ddbdc3c6ad9dadf50608b28e916c713d8584451ce072a9e17b8fd6d9a0fa7 | Python | 53,195 | 855 | """Run personalisation on the full 12-lead ECG beat recording"""
import sys
import multiprocessing
import os
# import time
from warnings import warn
import math
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from datetime import datetime
# import pymp
if __name__ == '__main__':
if len(sys... |
e7de29e39c971676eff2dd9be45243e2e47ae8464cbf3a843fe319ef4e21a593 | Python | 53,256 | 1,317 | #
# MIT License
#
# Copyright (c) 2023 GT4SD team
#
# 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 restriction, including without limitation the rights
# to use, copy, modify, merge,... |
dcfbc3064255196c4dedf4cbd8d379c31eda3d2f9878eacac9da3e4e207cdbeb | Python | 53,298 | 974 | import os
import multiprocessing
import random
import numpy as np
os.environ['TF_ENABLE_EAGER_CLIENT_STREAMING_ENQUEUE']='False'
import tensorflow as tf
from tensorflow import strings as tfs
import src.metrics as metrics
import src.utils
from src.losses import poisson_multinomial
from scipy.stats import zscore as zsc... |
73b8e798a154f432f14c95b451bc17b7a67d149a9b06556c580d50afdc5203fc | Python | 53,424 | 1,198 | """
pygments.lexers.python
~~~~~~~~~~~~~~~~~~~~~~
Lexers for Python and related languages.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import keyword
from pip._vendor.pygments.lexer import DelegatingLexer, Lexer, RegexL... |
e29c911695f6c7bdc7397d002925f5393a18efcaa0d8159e846351522ffe9f16 | Python | 53,490 | 1,254 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University 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 Lice... |
a4736a122739e540efe364710c2257685697392e1d8476ce77fd7fbb7a631a56 | Python | 53,603 | 1,351 | #morphoglia/morphometrics/builtin.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Morphometric extraction module for the MorphoGlia pipeline.
Single source of truth for:
- Canonical soma mask (distance-transform + global dilation)
- Whole-cell skeleton (true 1px, no pruning)
- Branches mask (cell minus som... |
e4d5f7eddb4cae924c36935048297bc5ed65c13aa3ffc714bb85b440505e2b43 | Python | 53,659 | 1,307 | # 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... |
cad4f69f77e797c3c6086b524fd12cf3b435f17d0e1ec551fe024e9a457b2406 | Python | 53,747 | 1,321 | # coding=utf-8
# Copyright 2020 The Facebook AI Research 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/LIC... |
542e03717e483f8835870ae4eb0f26ff24deb3d2d99f4bd18ff68ae044ac480c | Python | 53,847 | 1,315 | from __future__ import unicode_literals, absolute_import
from builtins import int, range, dict, zip
import os
import io
import re
import sys
import queue
# Future warning from cython in h5py
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import h5py
import numpy as np
np.seterr(all='... |
2634d8fcd7a3598aa7f6f0f069b8fdce7527c1820e3ced93a555459ab0c0ae13 | Python | 53,933 | 1,392 | # -*- coding: utf-8 -*-
import time
import numpy as np
import tensorflow as tf
from tensorflow.python.util.deprecation import deprecated
from .. import _logging as logging
from .. import files, iterate, utils, visualize
__all__ = [
'LayersConfig',
'TF_GRAPHKEYS_VARIABLES',
'flatten_reshape',
'clear_... |
f1b741cbff8099828d05bd99aafa1c16d873a4f0ea5d9e10857a1dc8594e8e5b | Python | 53,943 | 1,502 | # TODOs:
# - add parameter to use the "untyped" fraction in the clustering?
import re
import json
import functools
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.colors as mcl
import matplotlib.pyplot as plt
from pathlib import Path
from tqdm.auto import tqdm
# Fastcluster seems to b... |
d3c6c45bbff64bfa4585aaf1f38e2b95ae72b5f36edbf7f98c5efed1fd4d0a84 | Python | 54,050 | 1,053 | import math
import os
import platform
import sys
from pathlib import Path
import shutil
try:
import importlib.resources as pkg_resources
except ImportError:
# Try backported to PY<37 `importlib_resources`.
import importlib_resources as pkg_resources
import skimage
import cryovesnet
from . import pyto_scrip... |
8c2ca4d2f3910882d394de01ecd908174445d8c084790fb3fc06d22a49c9f299 | Python | 54,082 | 1,369 | # dcamapi4.py : Dec 16, 2022
#
# Copyright (C) 2021-2022 Hamamatsu Photonics K.K.. All right reserved.
import platform
from enum import IntEnum
from ctypes import *
# ==== load shared library ====
# abosorb platform dependency
__platform_system = platform.system()
if __platform_system == 'Windows':
__dll = wi... |
992fae4230700595e88ff754e400cdaa20871e76fa6fb1642e0a6187b6b5f543 | Python | 54,114 | 1,375 | # 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... |
1a1f7891d158d4bbfd86a38e1abd26ba657a79c98679549804bdcdd962cb8542 | Python | 54,128 | 1,466 | # 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... |
688d15730b8c94a876b2d3992235278205a5fd89deb85085a9c522a1e723de0e | Python | 54,241 | 1,255 | # coding=utf-8
# Copyright 2018 The OpenAI Team Authors and 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 copy of the License... |
230a349730102c7cb4e3778604ec2ee58d0c5adbf149a06d5b17d07adf5ae489 | Python | 54,309 | 1,320 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain 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
#
# U... |
daddfb9d64f079138bcbe2dca281d0b8d5846a93ecb6b514ea5998bc9768c09f | Python | 54,317 | 1,401 | ############################################################################################################
# Set of functions for reading the results returned by DisPerSe tools
#
#
__author__ = 'martinez'
import vtk
import numpy
import scipy
from astropy.io import fits
import math
try:
import pyseg.pexceptions
... |
f71643984170954faa0408bad87df04682576d39bc76f9db70e09ab39bce28d0 | Python | 54,481 | 1,471 | """
Contains class Contact for analysis of contacts between segments (from a
segmented image) and boundaries specified on the same image.
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import zip
fr... |
d4ced16a6c8594bc377c738041c9f66d763d607a476258c648cf6f8cf60a2df0 | Python | 54,618 | 1,537 | import gc
import os
from pathlib import Path
from typing import cast
import bpy
import nodebpy
from biotite import InvalidFileError
from bpy.props import (
BoolProperty,
CollectionProperty,
EnumProperty,
FloatProperty,
IntProperty,
StringProperty,
)
from bpy.types import Context, Operator
from .... |
5a521c94eaaeb16bce3928dcba144f41de518622481752d6d7f806fb6b36e5b2 | Python | 54,629 | 1,214 | import numpy as np
import torch
import torch.nn as nn
from torch import optim
from torch.utils.data import Dataset, DataLoader
from tqdm import tqdm
tqdm.pandas()
from itertools import product
import argparse
import random
import pandas as pd
import pickle
from typing import Union, Optional, List, Tuple
from collectio... |
75a8b4d04f24f914707515af511637cd24ebc8914174b3df4b6effebb90aa166 | Python | 54,684 | 1,095 | import datetime
import dill
from dreamcoder.compression import induceGrammar
from dreamcoder.utilities import *
try:
from dreamcoder.recognition import *
except:
eprint("Failure loading recognition - only acceptable if using pypy ")
from dreamcoder.enumeration import *
from dreamcoder.fragmentGrammar import *... |
5cfb5d0017ea2f3d02d8d621d2e19e28c5aa650f803da0ba5c8cdcda68a480c5 | Python | 54,740 | 1,576 | #!/usr/bin/env python
"""
There are two tasks preformed by this script:
1) An image is segmented using the hierarchical connectivity procedure
to yield connectors (segments).
2) These connectors are classified according the specified
classification criteria.
This script can be used to execute these two task... |
5edca131701cfe166caf6d7e2d208398b0a02b2469a658968de0ed9ae2294e3f | Python | 54,746 | 1,576 | #!/usr/bin/env python
"""
There are two tasks preformed by this script:
1) An image is segmented using the hierarchical connectivity procedure
to yield connectors (segments).
2) These connectors are classified according the specified
classification criteria.
This script can be used to execute these two task... |
1ad5ac35a8a9ec8f06c6dede6ebcae0c1216f2c602bdc58eafa3c5f1fed4718d | Python | 54,777 | 1,312 | # 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... |
b2f98c94516034aae209599032963deee306306dee3c7c64ebdef8b2711b3955 | Python | 54,787 | 1,217 | """Apply Transform tab - apply registration transforms to points and/or data.
Contains:
- ApplyTransformsTab(QWidget): accepts a registration output directory,
auto-detects transforms (ANTs/Elastix + Laplacian), and runs point
and/or data transformation in an external coloured terminal.
"""
import os
imp... |
ff54e9da71c1a868776701398f4c8c2401275a9f9b77344793334691b18388e5 | Python | 54,890 | 1,269 | # -*- coding: utf-8 -*-
"""
Created on Tue Dec 13 16:55:42 2016
@author: Laure Spieser and Boris Burle
Laboratoire de Neurosciences Cognitives
UMR 7291, CNRS, Aix-Marseille Université
3, Place Victor Hugo
13331 Marseille cedex 3
This file is part of Myonset.
Myonset is free software: you can redistribute it and/or m... |
f4358b5cb7735de783871fbfad1501c0d1cb3e1145dcb73aea144ff4efc948cc | Python | 54,949 | 1,352 | """Tests for the unified napari viewer module (regtools.utils.napari_viewer).
These tests exercise the pure-Python utilities (pad_and_stack, lazy_load_stack)
and verify import paths. Tests that require a running napari instance are
skipped in headless CI environments.
"""
import numpy as np
import pytest
... |
80daaad0f86941f9f2fe8b5aedbf1297d0310e8d832f3909af3ede27cd8dadea | Python | 54,971 | 1,119 | #!/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 dill
import os
import seaborn as sns
import re
from sklearn.decomposition import PCA
from sklearn.preprocess... |
827cec4456b8419d3620f5e2a0abdcbc641222c47043fa1f428646a5c21057dc | Python | 54,971 | 1,119 | #!/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 dill
import os
import seaborn as sns
import re
from sklearn.decomposition import PCA
from sklearn.preprocess... |
46bbf67222b8752da3e32ad66cebe95ef4ce441a664a49180f57c6d1e8abc396 | Python | 55,025 | 1,418 | ############################################################################################################
# Set of functions for reading the results returned by DisPerSe tools
#
#
import vtk
import numpy
import scipy
from astropy.io import fits
# import math
# from pyorg import pexceptions
import warnings
from pyto... |
2744906faa1af12fc1ef0eab2eb3e248e2539829e5737da81d200a529ce3db13 | Python | 55,055 | 1,228 | #
# Helper routines for working w/dask
#
# Copyright © 2020-2025 Ernst Strüngmann Institute (ESI) for Neuroscience
# in Cooperation with Max Planck Society
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
# Builtin/3rd party package imports
impor... |
2da5c2d264eeda94076abf93d13069f73a60deecba6a8695a1f5c7e710dc0733 | Python | 55,164 | 1,108 | # 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... |
a2e6e89a5588c75d62623ea0dcd9d1849b5d205e6c523fcda495f08f809efbc7 | Python | 55,174 | 1,113 | """
Performs Univariate 1st 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:
+ Plots by list:
* Univariate 1st order analysis against ran... |
7813761ccae6912c095a86ade8bf6dd9bb9352fe2f95e61f974c8be0e6eb85b9 | Python | 55,190 | 1,061 | #!/usr/bin/env python
# Copyright (c) 2019-2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides a parser for scenario configuration files based on OpenSCENARIO
"""
from distutils.util import strtobool
im... |
002309602865a18f83e9502b5c7c5dc18341c39bebec022cc4980261013ecc0b | Python | 55,264 | 1,230 | """
Utility functions for all our codes.
"""
import os
from os.path import join as joinP
import logging
import cPickle as cpk
import collections
import re
from bioservices import KEGG
from Bio import SeqIO
from Bio.KEGG import Enzyme
import networkx as nx
import matplotlib.pyplot as plt
import numpy as np
from scipy.... |
d3f177033500969c34b57c4618fea55f34ea1233cc09656103d2d12a44d17fe9 | Python | 55,268 | 1,219 | """
Find columns on synapse tomograms (ListTomograms) and measure their statistics.
Files for columns visualization in VTK format.
Input: - 3 STAR files (layers) with the ListTomoParticles pickles
Output: - Plots by tomograms and globally:
+ Number of columns
+ Column... |
655984d620a07a65c68f7da67ede83097ae6c180ba101c69ce6a0aadcc027501 | Python | 55,300 | 1,445 | import os
import warnings
from collections.abc import Sequence
from typing import Any, Literal, TypeAlias, cast
import matplotlib.pyplot as plt
import MDAnalysis as mda
import mdtraj as md
import numba as nb
import numpy as np
import pandas as pd
from Bio import SeqUtils
from MDAnalysis import Merge, transformations
f... |
b57ee72af594f50731337ed8768ded5476983dbb2b214dd299305d67dae1adda | Python | 55,321 | 1,181 | import numpy as np
import unittest
import pyntbci
FS = 120
PR = 60
SHIFT = 2
v = pyntbci.stimulus.make_m_sequence()
SHIFTS = np.arange(0, v.shape[1], SHIFT)
V = pyntbci.stimulus.shift(v, SHIFT)
V = np.repeat(V, FS // PR, axis=1)
N_CLASSES = V.shape[0]
CYCLE_SIZE = V.shape[1] / FS
LAGS = SHIFTS / PR
N_TRIALS = 3 * N... |
9aa94483c5d7ef3bea83b673429d46d1410672f7f0249f02240b16c654cb3d87 | Python | 55,367 | 1,369 | # coding=utf-8
# Copyright 2021 The I-BERT Authors (Sehoon Kim, Amir Gholami, Zhewei Yao,
# Michael Mahoney, Kurt Keutzer - UC Berkeley) and The HuggingFace Inc. team.
# Copyright (c) 20121, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use t... |
8e79394bf7faa0e568bac6d21f4d5287df9fc87cc39a4bf3c9e4f9ecac61e938 | Python | 55,438 | 1,644 | import itertools
from abc import ABCMeta, abstractmethod
from math import cos, radians, sin, sqrt
from pathlib import Path
import blf
import bmesh
import bpy
import gpu
import MDAnalysis as mda
import numpy as np
import numpy.typing as npt
from bpy_extras import object_utils, view3d_utils
from gpu_extras.batch import b... |
047ed1cf2bb32abc51356fdcac4f63acc0ae4f43b026ce116dc2d090368f0142 | Python | 55,502 | 1,200 | from __future__ import annotations
import copy
import math
import warnings
from collections import OrderedDict
from typing import TYPE_CHECKING, Any, Literal
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scanpy as sc
import seaborn as sns
from fast_array_utils.conv import to_dense
from... |
d292e2eeec80af721231005c737e9798654af2c1fdb7839d89e21f16f5f7945a | Python | 55,552 | 1,284 | # 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... |
a0ba88fe732020b453450908bbf9d902cba4a85de56546954d5cd06488f9f9d0 | Python | 55,578 | 1,600 | import sys
import os
import datetime
import argparse
import logging
import pickle
import glob
import subprocess
import logging
import inspect
import getpass
import random
import collections.abc
import re
import time
import tensorflow as tf
import imgaug as ia
import numpy as np
import h5py
import matplotlib.pyplot as ... |
54fc672e5d23559631555d9e38786b0d032f1f4f1b92309f35db11d3c063322d | Python | 55,609 | 1,399 | import PoseCommon
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
# from batch_norm import batch_norm_mine_old as batch_norm
if vv[0]==1:
from tensorflow.contrib.layers import ... |
f3320af97cb800e2faeb3b8f8f71a8e8251f4b5784fcde90073397c30dd6508f | Python | 55,642 | 900 | #!/usr/bin/python
# -*- coding:utf-8 -*-
import logging
import os
import time
import warnings
import torch
from torch import nn
from torch.utils.tensorboard import SummaryWriter
import numpy as np
import models
import datasets
from loss.focal_loss import FocalLoss
from utils.entropy_CDA import Entropy
from utils.entr... |
7e3c6e6aa539a88849a07d490922b5e6ed6c13cc658c75312c2137d1a24d11fa | Python | 55,679 | 1,283 | """ Module to extract low-dimensional properties from npx dataset;
plot population activity in pc space, both average and selected trials;
used get_data from glm_module.py module to load data id df divided by pre
and post drop;
Attention: load output of whisk_plot.py module, which return similarity of
whisker bouts fo... |
692d0f6f82a48fff1ac82cfc8220451a02ccfbc0e6518736a69d42f5d6cb956c | Python | 55,757 | 1,577 | import numpy as np
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui, QtCore
from pyclamp.gui.pyqtplot import *
import pyclamp.gui.lbwgui as lbw
from pyclamp.gui.pgb import pgb
from pyclamp.gui.xyfunc import *
from pyclamp.dsp.channel import chWave
from pyclamp.dsp.lsfunc import *
from pyclamp.dsp.wffunc import min... |
494040f5d09d77efcd1f28708b4d1d87ad4d08a6528ae2c35c9e13d53d7967f2 | Python | 55,761 | 1,187 | options = dict(
model_extensions=[
'h2o.model.extensions.ScoringHistoryGLM',
'h2o.model.extensions.StandardCoef',
'h2o.model.extensions.VariableImportance',
'h2o.model.extensions.Fairness',
'h2o.model.extensions.Contributions',
],
)
deprecated_params = dict(Lambda='lambda... |
532cb116245c3aabe5265f92c548ec64d90f8ac4f9989e660a406be030c44135 | Python | 55,899 | 1,208 | import inspect
from collections import deque
import torch
from torch import nn
from torch.nn import functional as F
from torch.utils import data as torch_data
from torch_scatter import scatter_max, scatter_add
from torchdrug import core, tasks, data, metrics, transforms
from torchdrug.layers import functional
from to... |
a65074147bd2aa7026fccbe0edaa50a77d08c4bfaf4f502607df412031e7c345 | Python | 55,974 | 1,227 | import PoseCommon
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
# from batch_norm import batch_norm_mine_old as batch_norm
if vv[0]==1:
from tensorflow.contrib.layers import ... |
5c82d02e9a6eb50379d7d52d4bcb78abe3b58a8e17ff093af2c5dfc1ae05686c | Python | 56,072 | 1,665 | #!/usr/bin/env python2
# Interactive script for the setup of dynamics calculations for SHARC
#
# usage: python setup_traj.py
import copy
import math
import sys
import re
import os
import stat
import shutil
import datetime
import random
from optparse import OptionParser
import readline
import time
from socket import ... |
144e49c3e087a2f4a39226f946177eb2919261972dbbcbedf7237eae37986eea | Python | 56,086 | 833 | """This script visualises the results from the inference of repolarisation properties from the T wave"""
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
if __name__ == '__main__':
if len(sys.argv) ... |
4d639f9bd9e9547973101e3a5b9bb87b6f121c68a42e54e1593ed1c2908a45b6 | Python | 56,092 | 1,096 | import copy
import csv
import gzip
import os.path
import pathlib
import platform
import shutil
import tempfile
import threading
import time
import traceback
import uuid
from queue import Queue
from shutil import copyfile
from threading import Thread
import pandas as pd
from boto3.s3.transfer import TransferConfig
from... |
3ee8eda553c8e15485a5449f0c25cc2f2094c3f54e3f877d6d5ee5259e5e766f | Python | 56,151 | 1,329 | import os
import torch
import pickle
import collections
import math
import pandas as pd
import numpy as np
import networkx as nx
from rdkit import Chem
from rdkit.Chem import Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
from rdkit.Chem.rdMolDescriptors import GetMorganFingerprintAsBitVect
fr... |
27cf5823f9769be0d3c2af2c318a1a9eebe58654de3ace4e032ff6d2f8a6487d | Python | 56,221 | 1,334 | """The maintainer's fitting tool and its review viewer.
Two halves, both exercised against SYNTHETIC atlases: the real volumes are
gitignored and absent from a clean checkout, and a test that silently skipped
itself on their absence would be no test at all.
* ``scripts/fit_hemisphere_planes.py`` - fits the inst... |
8cb3348b0708fbdd2892fb37d7aa1d57e4c9118540a91e77fd2bbe218ea743cf | Python | 56,339 | 1,655 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
902140e9e4a95f3454add8ca7f28dda621a2458b0a5e086a45d301f2b3056dff | Python | 56,348 | 1,433 | import requests as r
from Bio import SeqIO
from io import StringIO
import re
import pandas as pd
import numpy as np
from Bio import SeqIO
import uuid
import copy
import os
from Bio.PDB import PDBParser, MMCIFParser
from Bio.PDB import Superimposer
from Bio.PDB.PDBIO import PDBIO, Select
from Bio.PDB import MMCIFIO
from... |
efd07e8181720b33d3c7f353eeb2dd2d93228088d40737c651ee2638de9f4024 | Python | 56,462 | 1,303 | """
Set of classes for analyzing Synaptic Structural Columns
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 1.09.18
"""
__author__ = 'Antonio Martinez-Sanchez'
import vtk
import copy
import math
import numpy as np
import scipy as sp
from pyorg.surf import TomoParticles, Particle
f... |
3c63923558356115fec573d4e6254d018ceddb45a0c00d7cfe17d61bf3e73c70 | Python | 56,637 | 869 | 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 numpy as np
import pandas as pd
import scipy
import torch
from torch import nn, optim
import ... |
39afad051ddc72ee9672ec4976b2e70eecd64c8be3c232e69aa1cb930886bb6c | Python | 56,708 | 1,323 | """Evaluation of predicted survival curves for right-censored outcomes."""
from __future__ import annotations
import warnings
from functools import partial
import matplotlib.pyplot as plt
import numpy as np
from lifelines.statistics import logrank_test
from SurvivalEVAL.evaluations.calibration import (
d_calibr... |
c22715221ad310124d0375320ae6797a695fc4fa7dce0ba6a1b9b065d4e556f5 | Python | 56,803 | 1,376 | # Node-group asset "Style Cartoon" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
import math
from typing import T... |
309b571bb991db7038d029cb7473665c4c486b74a05de067401748a73f2486bb | Python | 56,882 | 1,712 | # 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... |
c7a36234ec1b8184c808af06a15a7292298883d4b9dc92b63c3119cbae9335f9 | Python | 56,986 | 1,730 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 3 13:14:05 2020
@author: Xingyan Liu
====================================================
Functions for downstream biological analysis
"""
import os
from pathlib import Path
from typing import Sequence, Union, Mapping, Optional, Callable
import logging
import numpy a... |
721a033c206fceda6ed69157b1c57567154db77b6b05c4ac67224406bf40be24 | Python | 57,042 | 1,098 | """Compare HED schemas and generate structured changelog reports.
This module provides tools for analyzing differences between HED schema versions or variants.
It supports fine-grained comparisons at the entry level (tags, units, properties, etc.),
detection of schema metadata changes, and structured changelog generat... |
8b7f3fa4371c853de56a573a107e64c272637abcc27750cf55e601019149d4a0 | Python | 57,116 | 1,330 | """Tests for the true-µm in-memory 2D registration path."""
import os
import sys
import numpy as np
import pytest
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
from regtools.registration.registration_2d... |
4e522fb180c5a42446a61ce6f77888ecc6b2feae4d84df5bf0657154059e1458 | Python | 57,548 | 1,457 | #
# This file is part of openCARP
# (see https://www.openCARP.org).
#
# The openCARP project licenses this file to you 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/lice... |
ea5a15086c7e464fc0e3876beb0245eab620a0f6142bde4b8f5c334804c31be9 | Python | 57,561 | 1,046 | #!/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... |
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