sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
369fdae3c3a8458f61ea5b43b32ec819705eebfe73d5be5f49549ff63753fb46 | Python | 6,439 | 160 | # Script to run simulations to evaluate effect of time-step
# on simulation accuracy and speed
from os.path import join
from get_paths import *
import matplotlib.pyplot as plt
import numpy as np
import cell_esser
import time as cookie
import lib_neuronsim
import multiprocessing
import multiprocessing.conn... |
cd45051aaa81dccca855ce47354bcd0c7d04a9d7860bedb75847833412dc59c2 | Python | 6,441 | 222 | # Copyright (c) 2023-2024 Blue Brain Project/EPFL
# 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 ... |
1b98e1b0fceb59e5d07a3eba77a6f60006d82c8865b7aaf9311581f0ff04159e | Python | 6,442 | 181 | # 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... |
7013d372b24e32fb3431bba62d623567bb0cadac0b800fd334e047453978775b | Python | 6,442 | 120 | """Prepare an induced, directed FlyWire circuit with explicit provenance."""
from __future__ import annotations
import hashlib
import json
import urllib.request
from datetime import datetime, timezone
from pathlib import Path
import numpy as np
import pandas as pd
from scipy import sparse
from scipy.sparse.csgraph im... |
9abadaca7651923efbead9a2bb48a58ef87225518e4d3d9e3d168219e4859c4f | Python | 6,442 | 164 | import os
import numpy as np
import pandas as pd
from scipy.io import loadmat
from sklearn.model_selection import train_test_split
from datasets.SequenceDatasets import dataset
from datasets.sequence_aug import *
from tqdm import tqdm
#Digital data was collected at 40,000 samples per second
signal_size = ... |
4eca804542610f64b2a7230f2f45de66ee61886c7c96d8a0bc3235058aa3836b | Python | 6,445 | 118 | """Neural interfaces: the mathematics between language-model activations and the reservoir.
Contract (duck-typed; see docs/PLUGINS.md, "Neural interface"):
hidden_size: int model hidden size the interface was built for
reservoir_neurons: int reservoir state dimension it reads
features: int ... |
e5afe1067963b305caecc0d62a8e7de3b76a638a408f7460d340ef716eca1482 | Python | 6,445 | 187 | from __future__ import annotations
from functools import cached_property
from typing import Literal
import numpy as np
import pandas as pd
from numpy._typing import NDArray
from scipy.stats import false_discovery_control
from sklearn.base import BaseEstimator
from sklearn.feature_selection import chi2
from cuppa.com... |
3b854f68f6f55b1f5668541813fe0ec51bc7c3b18e60cf50693a1ec10299a1cf | Python | 6,448 | 225 | # 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... |
3ec6d2c4b745a8adce22f7ced25b03613b19d9b1e17c941caf3a198bed44f1a7 | Python | 6,448 | 207 | # -*- coding: utf-8 -*-
#
# Syncopy object concatenation
#
# Builtin/3rd party package imports
import numpy as np
import h5py
import dask.distributed as dd
# Local imports
from syncopy import __acme__
from syncopy.datatype.continuous_data import ContinuousData
from syncopy.shared.parsers import data_parser
from synco... |
a6f24a9f71b16c95d142157e1bc7a87c09839caa6eab1c276423f1fefb06d727 | Python | 6,448 | 208 | # 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... |
6b71b171992033c14aff064aad82cec88fa4e59c6743949959dbd1c2112f288b | Python | 6,449 | 202 | # 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... |
abad71717ab8b668889abbdc4952d36c5c82883d85f8bffe8562866f3e32f2f8 | Python | 6,449 | 157 | """
requests.api
~~~~~~~~~~~~
This module implements the Requests API.
:copyright: (c) 2012 by Kenneth Reitz.
:license: Apache2, see LICENSE for more details.
"""
from . import sessions
def request(method, url, **kwargs):
"""Constructs and sends a :class:`Request <Request>`.
:param method: method for the ... |
56e804cf891a44e65a8956eccbb451299440428360e1e749b957f9bddf4fbe59 | Python | 6,450 | 184 | #
# MIT License
#
# Copyright (c) 2022 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,... |
e955595ac9042383630dfb0b4757250c12cae765af604792bcdd0055a243faca | Python | 6,450 | 191 | # 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... |
f8bf3680aa48bc8ed22c94e8ec9b7082da14c5a59546eace74d6baf649eb8cf2 | Python | 6,450 | 175 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import control.utils as utils
from control._def import *
import control.tracking as tracking
from queue import Queue
from threading im... |
bfd01aac4f22e6a3c24e196221fbe096cc6fe17ca294e5110e01e96cdac9bfdc | Python | 6,451 | 189 |
from pathlib import Path
import sys,os
import argparse
import logging
import sys
import typing as T
from pathlib import Path
from timeit import default_timer as timer
import torch
import esm
from esm.data import read_fasta
logger = logging.getLogger()
logger.setLevel(logging.INFO)
formatter = logging.Formatter(
... |
e5f131914daf44a41fc1b689cdb6b5d60653ac62fa4b9b4d063fcaa557e33504 | Python | 6,451 | 124 | import torch
import torch.nn as nn
class TSCeption(nn.Module):
r'''
Continuous Convolutional Neural Network (CCNN). For more details, please refer to the following information.
- Paper: Ding Y, Robinson N, Zhang S, et al. Tsception: Capturing temporal dynamics and spatial asymmetry from EEG for emotion r... |
e820382f5631c7dd6e07ff540627057116d3e9c36da9319a0b63713977b3572e | Python | 6,451 | 229 | """
This script computes the scores for the initial questionnaires according to the
each test's instructions.
Inputs: - excel file with the answers
Outputs: - excel file with the computed scores
@author: ana.trianahoyos@aalto.fi
Created: 07.06.2023
"""
import pandas as pd
from datetime import datetime
#########... |
e97427526a0e8f9e0f579ded1d4a671db98315a7284b20b7f5540de37057de39 | Python | 6,453 | 179 | ##### Useful functions used in the script #####
# Libraries
import numpy as np
import math
import operator
import functools
from scipy.stats import beta as betalib
import matplotlib.pyplot as plt
from scipy.special import gammaln
from scipy.stats import gamma, norm, invgamma
# Gamma pdf with parameters alpha, and an ... |
bac5a6b456113ac825c49ffcc01a6c4667534e351b326b368e27534eb2c91a5c | Python | 6,454 | 157 | import argparse
import json
import os
from openmm import XmlSerializer, unit
from openmm.app import PDBFile, StateDataReporter
from colabmda.openmm.modular.utils import (
add_solute_heavy_atom_restraints,
fresh_seed,
load_stage_state,
make_sim,
offset_seed,
save_stage_artifacts,
save_stage... |
5df4ff3dd3a05e5a2a7da86a7735625578448ccf1ae1e401f146dd3ee730c4bb | Python | 6,455 | 198 | from __future__ import annotations
import os
from logging import INFO
from pathlib import Path
import pytest
from ase.build import bulk
from ase.calculators.emt import EMT
from quacc import JobFailure, change_settings, get_settings
from quacc.runners.prep import calc_cleanup, calc_setup, terminate
def make_files()... |
d236df17c8a431f6f894fbb3d93bb74627806df2165d848b069738ac1fbc40ba | Python | 6,455 | 132 | import numpy as np
import os
import pandas as pd
from tabulate import tabulate
from constants import DATA_DIR, SCORE_COLUMNS
from src.preprocessing2.process_ratings import merge_rating_files
from src.utils import map_to_score_grid
ID_LENGTH = 24
def main():
ratings_clinicians = pd.read_csv(os.path.join(DATA_DIR... |
36293d3f24a61785782384fbf58392e9003af40b81ef63051a390368b8dbbf8d | Python | 6,457 | 162 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 13 09:57:27 2022
@author: Administrator
"""
import numpy as np
import os
import bigfish.stack as stack
import bigfish.detection as detection
import bigfish.multistack as multistack
import bigfish.plot as plot
from bigfishUI import *
from matplotlib import p... |
0ff06beae789a90768f6ffeefd852b8db963a9c45671c28f2b53d92e677c7195 | Python | 6,459 | 175 | # 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... |
b1bae1c72867b0e4d77d7c8c7167ae47c003e3137e44ce188e9bf301b9d561c2 | Python | 6,461 | 134 | import numpy as np
import numba
def simulateBOLD(Z, dt, voxelCounts, X=None, F=None, Q=None, V=None,
rho=None, alpha=None, V0=None, k1_mul=None, k2=None, k3_mul=None, gamma=None, k=None, tau=None):
""" Adopted function from neurolib, added parameters for the shape of bold activation to the argume... |
f60e59081b7765008d4cb3399a5f60a660017caae2dd2877fcc5d8b5ea02671b | Python | 6,461 | 138 | import numpy as np
import random
import pickle
import warnings
warnings.filterwarnings('ignore')
import numpy as np
from torch.utils.data import Dataset
class NetDataset_new(Dataset):
def __init__(self, mode, mech, args, min=None, max=None, ori_test=False):
super(NetDataset_new, self).__init__()
... |
aec71de8ecce1984ec8249934160f105c356c0ec92539f0001ae4083b2d464af | Python | 6,463 | 192 | """
Config file class
authors: Thomas Delemontex and András Ecker; last update 04.2023
"""
import os
import yaml
class Config(object):
"""Class to store config parameters about the simulations and analysis"""
def __init__(self, config_path):
"""YAML config file based constructor"""
self._con... |
f2e4de7d9efe8d1564edc72991d16483cee1526721682306b7448a560b049ee3 | Python | 6,465 | 99 | """DELETION_ANATOMY.py 2026-09-30. Pre-registration: 04-NOTES/PREREG-2026-09-30t-DELETION-ANATOMY.md
Where the synapses of Santos's antennal-lobe deletion lie (neuropil, sister projection neurons), and whether the deletion as
described (antennal lobe only, between glomeruli) does what the whole one does. usage: pyt... |
4c7bd507074e60c9140d1307ac8c511a35194f313feaa692498ffc2791afbe68 | Python | 6,467 | 186 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 10 18:49:13 2021
@author: tom, tong, melissa
"""
# TODO: Correct M1, M3, M5 (probably just scale by 43/401)
# TODO: Test and verify
import numpy as np
import cochlea
from mne.filter import resample
from joblib import Parallel, delayed
import ic_cn20... |
958aae47f594af74a0ae331e709f7708430bdb653480e850f3633cfa07088563 | Python | 6,467 | 153 | import sys
import inspect
import torch
# from torch_geometric.utils import scatter_
from torch_scatter import scatter,scatter_add
special_args = [
'edge_index', 'edge_index_i', 'edge_index_j', 'size', 'size_i', 'size_j'
]
__size_error_msg__ = ('All tensors which should get mapped to the same source '
... |
292878de2a983496bd06f88c0deb0c6e91373b1c2566aac26c079ae6143bfce1 | Python | 6,472 | 202 | import click
import einops
import torch
import torchvision
import matplotlib.pyplot as plt
import segm.utils.torch as ptu
import torch.nn.functional as F
from pathlib import Path
from PIL import Image
from segm import config
from segm.data.utils import STATS
from segm.model.decoder import MaskTransformer
from segm.mo... |
f6ca9a1aab309fa147c1edc861b308b19ce5ddefda5ee52e88bbe98bad491637 | Python | 6,472 | 168 | # -*- coding: utf-8 -*-
r"""This file implements a combination of the atomic charge (AC) and
the atomic dipole (AD) dipole model resulting in the AC+AD dipole model.
Atomic vectorial property predictions from the network are interpreted as
atomic dipoles while the atomic scalar predictions are interpreted as atomic
... |
48f29c9a36457bfc09c4a96b7f3518cac58e5c7a68744ab8aa10f594f070bdde | Python | 6,473 | 156 | #!/usr/bin/env python3
# Python standard libraries
import os, sys, filecmp, difflib, time, traceback, subprocess
# os.system('head -n 26 test_results.html> test_results.html.tmp && mv test_results.html.tmp test_results.html')
w="""
<html>
<head>
<title>Example tests results table</title>
<style>
th {
color: whit... |
7e9c4a6bae0a5ed1a17742437f76e3a5e20a0f9239f6e91c343e9af5de7b8690 | Python | 6,474 | 174 | import numpy as np
import random
from control_tools.common import adjust_trajectory, get_arm_prefix, generate_times
from pybullet_tools.utils import set_joint_positions, get_extend_fn, get_joint_positions, is_circular, \
joints_from_names, get_difference_fn
from pybullet_tools.pr2_utils import get_arm_joints, get_... |
2e51253b928b5f701fd5820e1621c2ea46076a1318e93408a49e885941507848 | Python | 6,475 | 155 | #!/bin/env python3
"""
Topology
--------
This submodule contains lots of functions to find the intersection of different kinds of sets.
"""
import numpy as np
from itertools import groupby
from typing import List, Tuple, Union
from scipy.interpolate import RegularGridInterpolator
from intersect import intersection
fr... |
0929d7f0f99fd683c29ddee3edb9f5fdfe7c1bd28736201b96f549e73ca437e0 | Python | 6,476 | 183 | import logging
import os
import shutil
from optparse import Values
from typing import List
from pip._internal.cache import WheelCache
from pip._internal.cli import cmdoptions
from pip._internal.cli.req_command import RequirementCommand, with_cleanup
from pip._internal.cli.status_codes import SUCCESS
from pip._internal... |
a9fe6809096a343cc5406f4358d17f4826f8244e981a6ff06309f13088777711 | Python | 6,476 | 155 | #!/bin/env python3
"""
Topology
--------
This submodule contains lots of functions to find the intersection of different kinds of sets.
"""
import numpy as np
from itertools import groupby
from typing import List, Tuple, Union
from scipy.interpolate import RegularGridInterpolator
from .intersect import intersection
f... |
cae0f6b236ed141cfb9a61f822192bfa3dfda0ca1a35f313d8fdf37f1624bd07 | Python | 6,476 | 198 | import argparse
import os, random, gc
import numpy as np
from numpy import *
import torch
import pickle as pkl
import time
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.utils import remove_self_loops, add_self_loops, subgraph
from utils.logger import Logger, save_result
from utils.dataset... |
fd2c40428fa4c6c2d4d09f88f45094305342dad97fdd9493da4f814e8b95f9ab | Python | 6,477 | 127 | from itertools import cycle
from control_tools.execution import ArmTrajectory, Detach, GripperCommand
from plan_tools.common import Control, Conf, Pose, get_reference_pose, is_obj_type
from plan_tools.samplers.generators import solve_inverse_kinematics, plan_waypoint_motion, \
compute_forward_reachability, check_i... |
6fcefdebea9f8e0fc5d58712b7b9703ff8e2668663c194af106201ef55ef5cb7 | Python | 6,479 | 153 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 21 16:47:06 2023
@author: deeperthought
"""
import os
import numpy as np
import matplotlib.pyplot as plt
import sys
MODEL_WEIGHTS_PATH = '/model/pretrained_model_weights.npy'
T1_POST_PATH = "/data/Breast_MRI_001/T1_axial_02.nii.gz"
DC... |
1c9c5fda4caeb5d4c04b41d41e25c1d9a0471f4a69716df5551554863a2e028f | Python | 6,481 | 150 | # Copyright (C) 2024 by mao jiashun and wang jianming
# Copying and distribution is allowed under AGPLv3 license
# This script implements the training of a WGAN (either WGAN-CP or WGAN-GP) on molecular data,
# leveraging graph neural networks (GNN) for 3D molecular structure representations and SMILES-based data.
# Th... |
2d7f72916871f98ac0cb9774380f99bdb51d3f8a0c7640fd6a6d364ac0cab71c | Python | 6,481 | 183 | # 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... |
ff68fa50931290a3ce69cedc754cacca75accf9ec165f1120700e32da50f5def | Python | 6,484 | 172 | """Smoke + signature tests for previously-untested cell_counting_legacy.
The module is deprecated for new development but process_counts and
update_summary_structures are still imported by point_registration.
load_summary_structures is already covered in
test_cell_counting_legacy_count_labels.py; this file adds... |
e45660123d05f81eabf2a6910495c12a8e7de02be1a864bffd58f640aff66710 | Python | 6,485 | 168 | """Regression guards for the batch-2D improvements: hard cancel, per-image
timeout, stop-on-failure, retry/resume, deterministic progress, real Align
template, and log-capturing .bat lines.
"""
import os
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
import numpy as np
import pytest
from unittest.moc... |
a9e413ea34265a233c67007dac86e74cffb640b0f808022e16bc3fa6d602d47a | Python | 6,487 | 233 | # 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... |
2d5d4136e36166e7574d7f72c88f2820fcc5b204fb8aa80215fcf23baae6e762 | Python | 6,488 | 157 | # 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... |
4f9da2effee7d9b184a0f56027d2e5dd9e7619f996c99b891d922fe14f6f0375 | Python | 6,488 | 241 | """Data type definitions for the sleeplab format."""
import numpy as np
import zarr
from collections.abc import Callable
from datetime import datetime
from enum import Enum
from functools import cached_property
from pydantic import BaseModel, Field, model_validator
from pydantic.functional_validators import AfterValid... |
c2f1d5c5c3606be1739b0c57f6c04882c26e899ea5dccd34f2d8af76be8e2c5e | Python | 6,488 | 181 | import pandas
import rtree
import networkx
import numpy as np
import cv2
from skimage.measure import regionprops
from functools import reduce
from merlin.core import analysistask
from merlin.util import imagefilters
"""
A module for sequential round analysis
Latest Update: Rongxin Fang 11/12/2022
"""
class SumSignal... |
f4a7bc7e84642c3fcac8ae4170b8cfe90f6b5d43818da4344d581270712689ac | Python | 6,488 | 134 | """
SIZE_MATCHED_BOOTSTRAP.py - written 2026-09-14.
WHY THIS EXISTS. V-66 ticked the figures and then said, in its own words:
"LIMITATION, stated: these ratios have no confidence interval yet. ... a bootstrap
over neurons is still owed before they go in print."
This is that bootstrap. It pays the debt... |
1415bdd868fa6beb5c74a9240e86b6305b11f9e2226f7675845e7a459c3650e6 | Python | 6,489 | 197 | import os
import shutil
from pathlib import Path
from time import sleep
import elasticai.experiment_framework.remote_control as eaixp_rc
import pytest
from elasticai.experiment_framework.synthesis.vivado_synthesis import (
_run_synthesis,
)
from hypothesis import HealthCheck, given, settings
from hypothesis import... |
a4e396f25c943722f28951edc7886a4845f97cd3e26084c361f62b3cda268afa | Python | 6,489 | 213 | # -*- coding: utf-8 -*-
"""
Created on Jun 05 2023
@author: Jonas A. Thiele
"""
###Read results of models trained with network-specific links on the main sample (610 subjects) via 5-fold cross-validation
import numpy as np
import scipy.stats
from sklearn.metrics import mean_squared_error
from sklearn.m... |
a3319619ab0623bcc9e0cc5bd7fc4641c56a81f9b283fe3bc0b404b8c2e79b55 | Python | 6,491 | 286 | from .extend import (
Box,
SparseObject,
VSpace,
defjvp,
defjvp_argnum,
defvjp,
defvjp_argnum,
notrace_primitive,
primitive,
vspace,
)
from .util import subvals
isinstance_ = isinstance
isinstance = notrace_primitive(isinstance)
type_ = type
type = notrace_primitive(type)
tupl... |
425d7df5130199db250ae6d3a8d4be3c69cb2f4541fdb92ec036068b8b1b275f | Python | 6,492 | 141 | from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.nn.integer.LUT.design import LUT as LUTDesign
from elasticai.creator.vhdl.auto_wire_protocols.port_definitions import create_port
fro... |
239cbc848b87fff7cbf4e86ab84cb58d981c3df1fa59ba525851f7c2d996e103 | Python | 6,493 | 227 | import time
from tqdm import tqdm
import numpy as np
from scipy.stats import spearmanr
from sklearn.metrics import roc_auc_score
import torch
import torch.nn as nn
from torch import Tensor
from torch.optim import Adam
from .ptgwas import PTGWAS
from .predictor import get_predictor
def lowrank_plus_diag_solve(W, d,... |
cb0c0fed48f3c52febbf849f880203104d20699e873888341cb83fe67232c11f | Python | 6,493 | 130 | # Import the necessary packages
import argparse
import anndata
import pandas as pd
import numpy as np
import os
import random
from collections import Counter
from pybiomart import Dataset
import re
# Define argument parser
parser = argparse.ArgumentParser(description="Process arguments.")
parser.add_argument("--inputP... |
041b92ca6e1232834fa81a9bebd6a095a33dcd97c382a4d6733888d1ee4e751d | Python | 6,494 | 173 | # Node-group asset "Color VMD" (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.
from typing import TYPE_CHECKING, Li... |
26b20c57f96d924b466bc97c4615adcf5dc2df775a5a980f5db75ac766399cb8 | Python | 6,494 | 194 | """Headless threading tests: effort/overrides reach ants.registration kwargs.
ants.registration is monkeypatched to a recording stub, so no real
registration runs. Verifies the 2D kernel merges resolve_ants_kwargs output
into the reg_kwargs dict it passes to ANTs.
The kernel does ``import ants`` at function sco... |
49005d91ab574a280a186fd2683d14d29d49c1d7eb836e9408d7078245d97dd0 | Python | 6,494 | 150 | import logging
from typing import Iterable, Set, Tuple
from pip._internal.build_env import BuildEnvironment
from pip._internal.distributions.base import AbstractDistribution
from pip._internal.exceptions import InstallationError
from pip._internal.index.package_finder import PackageFinder
from pip._internal.metadata i... |
6597b7a7a7f9455d3350c4ed0270a20847886fdadc39b2c3eba122b2c108ed5f | Python | 6,496 | 200 | # 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... |
51f8537afe8e8283350b9a7a119004e3f1c649f7e7915706bfbf2027076fea71 | Python | 6,497 | 194 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..initializer import create_initializer
from ..functions.shake_shake_function import get_alpha_beta, shake_function
class ResidualPath(nn.Module):
def __init__(self, in_channels, out_channels, stride):
super().__init__()
sel... |
96c42cc897b5d4604d23229829cb91c7fef172c6108a0322fc4632f2c1bbecb8 | Python | 6,497 | 178 | ##### Useful functions used in the script #####
# Libraries
import numpy as np
import math
import operator
import functools
from scipy.stats import beta as betalib
import matplotlib.pyplot as plt
from scipy.special import gammaln
from scipy.stats import gamma, norm, invgamma
# Gamma pdf with parameters alpha, and an ... |
a236cc323bf5926a293c4c7d2027a0e7b2b96eaf0f7449cfceb35bc24c8fc9c9 | Python | 6,499 | 195 | import warnings
from collections import defaultdict
from contextlib import contextmanager
from typing import ClassVar
import numpy as np
import autograd
from .util import subvals, toposort
from .wrap_util import wraps
def trace(start_node, fun, x):
with trace_stack.new_trace() as t:
start_box = new_box... |
511b77000f9fde50cef4e430f13b936a7869ff8fdcf292303ee91550525f090b | Python | 6,500 | 134 | import importlib.resources
from sitetack.app.alphabet import Alphabet
from sitetack.app.kmer import Kmer
from sitetack.app.predict import Predict, SitePrediction, SequencePrediction, SequencePredictions
from pathlib import Path
from sitetack.app.enums import PtmKind, OrganismKind, LabelKind
from sitetack.app.sequence i... |
a0e73d7cfc26bf2f7f4d40751babdcc1c254071103748ac40593fc043b26044b | Python | 6,501 | 176 | ###
# This file will:
# 1. Generate and save Alexnet features in a given folder
# 2. preprocess Alexnet features using PCA and save them in another folder
###
import glob
import torch
import InternVideo
import numpy as np
import urllib
import torch
import cv2
import argparse
import time
import random
fro... |
cd7a46487e9817ebc4c6645cf7944f1fb9593ec5920a5e60e64f84b76b29c673 | Python | 6,505 | 150 | import argparse
from loader import MoleculeDataset
from dataloader import DataLoaderMasking #, DataListLoader
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from tqdm import tqdm
import numpy as np
from model import GNN
from sklearn.metrics import roc_auc_score
from ... |
0877e61fd6a45bfcb9c43f48d565c387dfe30677ac2c6af51eafda8fea2900c5 | Python | 6,506 | 128 | import os
import pickle as pkl
from typing import Any, Callable, Dict, Tuple, Union
from ..base_dataset import BaseDataset
class MemoryAgeDataset(BaseDataset):
r'''
Args:
root_path (str): raw data files in pickled python/numpy formats
# ----- for IO -----
io_path (str): The path to g... |
00fbef853db2e43b22107577ed9edfe0efc1d8393e16a0c55fef9e68b59661b7 | Python | 6,507 | 202 | # -*- coding: utf-8 -*-
"""
Created on Thu Dec 8 20:46:46 2022
@author: Dustin Garner
"""
import os
import math
import numpy as np
import pandas as pd
from matplotlib.colors import ListedColormap
from fafbseg import flywire
import flycode.utils as utils
def import_file(file_name, sheet_name=0, usecols=None,
... |
ddc233f49ed7427338561f7791a588749325b92554251c4c527b5ed453d34e7e | Python | 6,508 | 201 | # 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... |
4b75ee3d957b99489bc47b3982d4dd45229b03b9afe0e8b70ab2a6aeaf14a112 | Python | 6,509 | 165 | import warnings
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
import pytest
from SurvivalEVAL import IntervalCenEvaluator, SurvivalEvaluator
from SurvivalEVAL.evaluations.calibration.distributional import (
coverage_ic,
create_censor_hist,
create_interval_c_h... |
8ad1eaa276cb2de738ea9007c021559815f097e4221ab7704b314651aa07a069 | Python | 6,510 | 134 | # -*- coding: utf-8 -*-
import torch
from supar.models.dep.biaffine.model import BiaffineDependencyModel
from supar.structs import DependencyCRF, MatrixTree
class CRFDependencyModel(BiaffineDependencyModel):
r"""
The implementation of first-order CRF Dependency Parser
:cite:`zhang-etal-2020-efficient,ma-... |
9210a25ca60e6129428bf3b5b28e09bab6f56bb8c9f813e6ecbb9d028e21c77d | Python | 6,517 | 206 | # 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... |
fd4c1a8f10ec08d85b02870d4f2daba821e3b39fe10c0352f3567a8dfd31032a | Python | 6,518 | 167 | import numpy as np
from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.nn.integer.ram.design import Ram
from elasticai.creator.vhdl.auto_wire_protocols.port_definitions import create_p... |
74e0e83387c2074098d7608f0db4299c492de710aba4d421fe6993ee5b3df56a | Python | 6,519 | 221 | """Computes the extraction efficiency in 3D and cylindrical coordinates.
Verifies that the extraction efficiency of a point dipole in a dielectric
layer above a lossless metallic ground plane computed in two different
coordinate systems agree.
"""
import matplotlib.pyplot as plt
import meep as mp
import numpy as np
... |
5de5847042842112a1b9db8ae7eb824fdc2e966b6db8c5bc09a09aa2e052f1b7 | Python | 6,520 | 147 | from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.vhdl.auto_wire_protocols.port_definitions import create_port
from elasticai.creator.vhdl.design.design import Design
from elasticai.c... |
b651fba6416303641528aaa1a773885c61fd8b0c21081524c30f60f85e0eb93d | Python | 6,520 | 179 | import numpy as np
from matplotlib import cm
import matplotlib.pyplot as plt
def plot_cycle_timeOfday (time_x, time_x_names, daily_var_dayAvg, roi_names, ylabel, fig_title, is_avg_plotted = True,tick_Hfreq = 2, ax=None, ylim = None, outcome_clrs=None, clr_avg = None):
[n_roi, n_win] = daily_var_dayAvg.shape # ... |
b2794f5ff46221a66ad3e28e13a1ea0f8291c7834592bff1cae077c9b8e916b3 | Python | 6,522 | 205 | #!/usr/bin/env python
#
# Copyright 2006, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
bff0645ca7d355f34f435659fcff2bf79cf51a4c15ef68df90a5d94bda36929e | Python | 6,522 | 179 | # 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... |
9b3cfdb4da184bb40ee83fa321a83d225b0f8b0df00597a164aef0d9760558a1 | Python | 6,524 | 183 | # 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... |
5492adc29d61adb332b40080f56fe65d246b0312f9e65c72fa709fdc02dba778 | Python | 6,525 | 213 | # 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... |
418fd2afbaa74f1f37b11334fe6fa7a7aac0d21b7bdde658fa5dff428d683823 | Python | 6,526 | 160 | # Node-group asset "Offset Point Along Curve" (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.
from typing import TY... |
83820212bd94d149fd7db416ab302062035a375427be8c5b1eedc1778da59787 | Python | 6,527 | 214 | ##
# \file niftyreg.py
# \brief Class to use registration method NiftyReg
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date Aug 2017
#
# Import libraries
import os
import numpy as np
import SimpleITK as sitk
from abc import ABCMeta, abstractmethod
import pysitk.python_helper as ph
import ... |
f0bcc7f9c26bacf3af580e88e5c3e3fd83a39cd3bc96f79f02639f2baae63be7 | Python | 6,535 | 157 | """``axisAlignData`` now finds the midsagittal plane by reflection symmetry
(``regtools.hemisphere.fit_from_image``) instead of Hough-line fissure
detection. These checks pin the new seam: the plane->normal conversion plus the
rotation must (1) be a no-op when the moving volume already matches the
template, and (2)... |
f56ddeb2a10d4c909f4a2b5b3a43d881270940564231ec67c41463fe05af2408 | Python | 6,535 | 188 | # gff class
import pickle
def extract_region_by_attri(gff3_eles, attri_name, attri_val):
outstrs = []
for gff_ele in gff3_eles:
if attri_name in gff_ele.get_attr_keys() and gff_ele.get_attrs()[attri_name] == attri_val:
outstrs.append(gff_ele.print_str())
print("extract {} regi... |
1ceda0ecf571492e5409c0e8bf781e668e6d08c8365d033a852796a98729d855 | Python | 6,536 | 247 | import numpy as np
from numpy.testing import assert_array_almost_equal
def unbiased_edge(x, y, p_minus, p_plus):
z = (y - (p_minus - p_plus)) * x
return z / (1 - p_minus - p_plus)
def unbiased_mean_op(X, y, p_minus, p_plus):
return np.array([unbiased_edge(X[i, :], y[i], p_minus, p_plus)
... |
73941240a2af0f7afe18274be293302cf8a02e84ce1afb3baa6456dcb8d7a9ad | Python | 6,536 | 186 | # -*- coding: utf-8 -*-
"""
Created on Wed Aug 2 14:43:18 2023
@author: ashwin.bhandiwad
"""
import os, subprocess
import pandas as pd
import numpy as np
import json
import matplotlib.pyplot as plt
import requests
import SimpleITK as sitk
import pathlib
import anndata
def plot_section( xx, yy, cc=None, val=None, fi... |
77edcc949f1ec0889b5dd670c05054cc0cafdb179e46fed23f2b8eab71ab0237 | Python | 6,536 | 197 | from __future__ import annotations
import os.path
import pandas as pd
from cuppa.logger import LoggerMixin
from cuppa.misc.utils import check_required_columns
class CuppaFeaturesDir(LoggerMixin):
def __init__(self, directory: str):
self.directory = directory
FILE_PATTERNS = dict(
snv="cupp... |
81d8c57f9f22d8315ea322b91df6c8c793dca60dba3a41c88c898eb15ba3800c | Python | 6,537 | 149 | import numpy as np
import pytest
from regtools.tilt_slice.oblique import extract_oblique_planes
def test_zero_tilt_equals_plain_coronal_slice():
rng = np.random.default_rng(0)
vol = rng.random((60, 40, 50)).astype(np.float32)
idx = 25
inten, labels = extract_oblique_planes(vol, None, idx, 0.0... |
53c80b9b58bdf50706cd7c5a704b9fb0878daa10ed1dfc0a2e1369920a885c8d | Python | 6,538 | 147 | ###############################################################################
# This code generates the missing data plots for behavioral data. #
# #
# If plotting data from the first pilot, use the following values: #
... |
54bd229afa34cd3ea0e29860ba5fec4829bdabcd4e8e93b2bf9aeee5b883dc39 | Python | 6,541 | 138 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
3576343621b6c17e58a5dfc93f8d335e035f6283b7e83aa49d133b4b32cc9b84 | Python | 6,542 | 147 | import argparse
import random
import sys
import numpy as np
import os
import pandas as pd
from pathlib import Path
from tabulate import tabulate
import json
import torch
from constants import *
from src.dataloaders.rocf_dataloader import get_dataloader
from src.models import get_classifier
from src.training.train_uti... |
90c67ebd99e61c0157399c03b193ddbd36c6e5575d6f226b4125f8a6518d4c49 | Python | 6,542 | 174 | import sys
import os
import json
import neo4j
import pandas as pd
from ckg import ckg_utils
from ckg.graphdb_builder import builder_utils
def read_config():
try:
ckg_config = ckg_utils.read_ckg_config()
cwd = os.path.dirname(os.path.abspath(__file__))
path = os.path.join(cwd, 'connector_co... |
6eba6cc7e128ea5a6b30c9a05c183fe8a0b6fd5012dc9013b8f390704de8259f | Python | 6,543 | 150 | #!/usr/bin/env python
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Collection of traffic scenarios where the ego vehicle (hero)
is making a left turn
"""
from six.moves.queue import Queue # pylint: disable=relative-import
import py_trees... |
14f628c9572a6f66dd629b5ed59c423024d328fb6778d71d07ae0fe4172eecf0 | Python | 6,545 | 173 | from __future__ import division, print_function
import numpy as np
__author__ = "Marcos Duarte, https://github.com/demotu/BMC"
__version__ = "1.0.4"
__license__ = "MIT"
def detect_peaks(x, mph=None, mpd=1, threshold=0, edge='rising',
kpsh=False, valley=False, show=False, ax=None):
"""Detect pea... |
8327ad343b17512be371ebcf2ea0cca7c09add5cfab278f8b6529441511f1de8 | Python | 6,546 | 155 | from __future__ import print_function
import os
import sys
import time
import math
import random
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import torch.backends.cudnn as cudnn
from torchvision import datasets, transforms
from datasets import list_dataset
from datas... |
cef14fb0c2b4b05691825d3eb34fe0a45c6c6b3a5b1b76e51eeca5f62bde7de9 | Python | 6,546 | 199 | # 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... |
d56d25a947a3e8c6775b3363ed5e2d0a7c23fb397ecf82dc236434cc1380b444 | Python | 6,546 | 198 | # 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... |
7e074c63d15a3ddf7d0a6e2bcba5fee76d41f2bc295c4be67ee2fe7532cf695f | Python | 6,547 | 151 | import unittest
from hed.errors.error_reporter import ErrorHandler
class TestFilterIssuesByCount(unittest.TestCase):
def test_empty_issues_list(self):
issues = []
result, result_counts = ErrorHandler.filter_issues_by_count(issues, 2)
self.assertEqual(result, [])
def test_all_below_li... |
42b341889ba4736e04bea323e826342bc92c8a42cc17baac44e4cf75d6d1ac95 | Python | 6,548 | 187 | import os
import pickle
import bct
import numpy as np
from time import process_time
from strength_preserving_rand_rs import strength_preserving_rand_rs
from strength_preserving_rand_sa import strength_preserving_rand_sa
from strength_preserving_rand_sa_energy_thresh import strength_preserving_rand_sa_energy_thresh
fr... |
76257f849ce06f43e99d3f9423cbf8d11636aec98bb67f05c5a835f332676b61 | Python | 6,550 | 203 | """Run decoding pipeline. """
from __future__ import annotations
import pathlib
import time
from collections.abc import Sequence
from typing import Annotated, Literal
import pte
import pte_decode
from pytask import Product
import motor_intention.project_constants as constants
PATHS_STIM_OFF = tuple(
constants.D... |
7829f61a03e6c79b28baade9625494dc0c8de9a8b625ccb39e7d4ce6e4030261 | Python | 6,551 | 225 | # 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... |
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