sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f6dfb8c31348d0bc6350672135eca7ac4a560ea5297993f91f61cb838a77e9f8 | Python | 8,472 | 203 | #! /usr/bin/env python3
"""Smoke-test a pose-estimation environment/image end to end.
Runs the mmpose top-down demo on a fixed input image and compares the rendered
result to a known-good target image, passing/failing accordingly. On success
the rendered output image is deleted; on failure it is left for inspection.
... |
b84b33df89550996d2f44874af52ca67e72f757a25f34a0335d174b86d731f03 | Python | 8,474 | 278 | # 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... |
d7b266080cfa7e0feaecfe6bfef6fb762d3a4a6a55510703fd88b249fc3e8fb9 | Python | 8,477 | 175 | # 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... |
155fb5f650d4691e38a0ddbb82d362ee757d9d046ede22e002a52bacfc2ecbff | Python | 8,478 | 211 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 10 14:17:59 2020
@author: asong
"""
from layers.DiffractiveLayer import Diffractive
# from layers.DiffractiveLayer import Diffractive , DiffractiveLayer
from layers.MaskLayer import PhasePlate, OpticalElement, AmpPlate, SuperPlate #, PhasePlateScaled
# from layer... |
4d3f2c6fd3d39ec9ca861ac6b8790b3748dd37476d2a1b4f904afd0a27436cf3 | Python | 8,478 | 274 | import colorsys
import io
from time import process_time
from pip._vendor.rich import box
from pip._vendor.rich.color import Color
from pip._vendor.rich.console import Console, ConsoleOptions, Group, RenderableType, RenderResult
from pip._vendor.rich.markdown import Markdown
from pip._vendor.rich.measure import Measure... |
92a7f3e145c88cf1b73f047717b2cb4ce51b4236d3b604d80f4ae88edd2723ea | Python | 8,480 | 268 | # IMPORTS
import os
from argparse import ArgumentParser
import pytorch_lightning as pl
import torch
import collections.abc as container_abcs
from pl_bolts import _HTTPS_AWS_HUB
from pl_bolts.models.autoencoders.components import (resnet18_decoder,
resnet18_encoder,
... |
e5733c961aaf21616b3550ca03b59614d5e5c727c021fad4f5db3a428b3680a4 | Python | 8,481 | 295 | import numpy as np
import scipy.special as sp
from .from_gpaw.spherical_harmonics import Y
'''
Real spherical harmonics follow the definition:
https://en.wikipedia.org/wiki/Table_of_spherical_harmonics#Real_spherical_harmonics
Work functions for generating spherical harmonics are adapted from GPAW
'''
def sp... |
b8593d5850979e07a06201466ce1e172263f066dfa7d9db6a97d8144ca1143ca | Python | 8,482 | 241 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import pathlib
import string
import torch
from esm import Alphabet, FastaBatchedDataset, ProteinBertModel, pretrained, MSATr... |
2a3325c8315d80cbf68085978b929b13843f4172fe13553c4c5eb8c84b4a1fc2 | Python | 8,484 | 202 | import os
import argparse
import lxml.etree as ET
import numpy as np
import carla
from utils import ALL_TOWNS, \
parse_annotations_file, interpolate_trajectory, scan_route_for_scenarios
ID_START = 0
PRECISION = 2
SAMPLING_DISTANCE = 30
def main(args):
scenarios_list = parse_annotations_file(args.sc... |
030f33350ef2bc7683a4556d232640b8e8584c8c620c41a64540c670c93b9d55 | Python | 8,486 | 230 | # 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... |
4bb1608914587d46f25985fa5849f67c366fae4b5fd0d46e3f354812c2537777 | Python | 8,488 | 221 | """
Shared QMainWindow base class for all Xu Lab pipeline launcher GUIs.
Eliminates ~120 lines of duplicated boilerplate per launcher by providing:
- Window geometry, icon, and stylesheet setup
- Standardized header/footer labels
- QApplication bootstrap with font and taskbar icon
"""
import os
import sys
... |
fa5453b1ce6a8d3f179a123d0643f9332a012d6274bbd7a635af806344112782 | Python | 8,488 | 252 | """
Script for segmenting the filaments in a tomogram without assuming any geometric constrain
(old version because it does not use MCF classes)
Input: - Original tomogram (density map)
- Mask tomogram (0-fg, otherwise-bg)
Output: - vtkPolyData with the filaments
- Segmentati... |
08ad4c6c35b7190983be2a4708c35eedc4a10fb64d065b6a76332af9147cb01b | Python | 8,491 | 185 | import pickle
from neuron import h
from abstract_circuit import AbstractCircuit, AbsCell, AbsSegment, AbsConnection
import os
import json
import copy
def load_json(file_name):
with open(file_name, 'r+') as f:
data_dic = json.load(f)
return data_dic
def pkl_new2old(config_file, src_file, dst_file):
... |
d8c6903adb950e64ec1c68ddf1dd5c47d01ad4a658e3a2b54bdbcb58ab7ecef0 | Python | 8,491 | 241 | # 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... |
01008758de04abdc6ed8f808334ea891eca39dfe4b225948da2bf915c669cf56 | Python | 8,495 | 322 | """
MatPES-compatible recipes
!!! Important
Make sure that you use the MatPES-compatible pseudpotential
versions (i.e. v.64)
"""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from monty.dev import requires
from quacc import flow, job
from quacc.ca... |
4463198042aabd4f342c84012ad8dfcf856d781eda9526a3873ae4bedccb9c34 | Python | 8,498 | 232 | import bpy
import MDAnalysis as mda
import numpy as np
import pytest
from databpy.object import LinkedObjectError
import molecularnodes as mn
from molecularnodes.entities.molecule import oxdna
from .constants import data_dir
pytestmark = pytest.mark.filterwarnings(
"ignore:.*no reference attributes.*:UserWarning"
... |
fba6f8da8ecd54d35f5b11f92c4906c03068ea1be641aecb3a6cd4373f8cb299 | Python | 8,498 | 211 | import numpy as np
import unittest
import pyntbci
FS = 120
N_TRIALS = 11
N_CHANNELS = 7
N_SAMPLES = 2 * FS
N_CLASSES = 5
N_COMPONENTS = 3
class TestCCA(unittest.TestCase):
def test_X2D_Y2D(self):
X = np.random.rand(N_SAMPLES, N_CHANNELS)
Y = np.random.rand(N_SAMPLES, N_CHANNELS - 1)
cca... |
8d55c0ff6e75d598977440dd3b20bbe48b0aef889bb15d3283d0cfd6125d4eeb | Python | 8,501 | 214 | from typing import Union, Dict
import numpy as np
from ..base_transform import EEGTransform
import scipy
from ...utils import LazyLoader
class Downsample(EEGTransform):
r'''
Downsample the EEG signal to a specified number of data points.
.. code-block:: python
from torcheeg import transforms... |
9608109a5325767d79a924849347042b727bae722d2bf55ddec251d94310f006 | Python | 8,502 | 249 | # 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... |
db06c2d8d5ef1039d8abf004028177dd6c01d4cb71ac12844fef94846d87986c | Python | 8,503 | 279 | # -*- coding: utf-8 -*-
#
# Test resampledata
#
# 3rd party imports
import pytest
import inspect
import numpy as np
import matplotlib.pyplot as ppl
# Local imports
import dask.distributed as dd
from syncopy import resampledata, freqanalysis
from syncopy import synthdata
import syncopy.tests.helpers as helpers
from s... |
dc7b9c3279352e3f5322a7d0b6238a06d7357fbb5baa4376bb17d1c1f30b011d | Python | 8,504 | 213 | # try searchlight decoding to classify different task representations
# based on https://nilearn.github.io/dev/auto_examples/02_decoding/plot_haxby_searchlight.html#sphx-glr-auto-examples-02-decoding-plot-haxby-searchlight-py
import numpy as np
import pandas as pd
from nilearn import datasets
from nilearn.image import... |
a70d5ea4674c8f58431a20aed401eaab33847e35fc3157625bb3b50654fcf9e4 | Python | 8,505 | 225 | ######################## BEGIN LICENSE BLOCK ########################
#
# Contributor(s):
# Jason Zavaglia
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the ... |
8fa3c73e611ad774f59c85c3eee2d516a2a9852cfaa010690f6d4c59aa6c8ee4 | Python | 8,507 | 194 | import os
import numpy as np
from pandas import read_csv, DataFrame
from pyrelimri.icc import sumsq_icc
def triang_to_fullmat(corr_1darray, size: int):
"""
Convert a 1D array representing the lower triangular part of a correlation matrix (including diagonal)
into a full NxN correlation matrix.
Parame... |
da6e7e05625849ac9737f3202c9b744342bf1b0502535852fdb3f3dfca52cf1f | Python | 8,507 | 236 | import os
import sys
import torch
import numpy as np
import cv2
import matplotlib.pyplot as plt
from PIL import Image
import re
import csv
# Set matplotlib backend
import matplotlib
matplotlib.use('TkAgg')
# Use bfloat16 for the entire script
torch.autocast(device_type="cuda", dtype=torch.bfloat16)._... |
1089e54d89e1f6237efe74bd2e6bac5a35a19f964ebc7709c4d97d8641eb24f1 | Python | 8,509 | 289 | import random
import numpy as np
import torch
from wsilearn.utils.cool_utils import hwc_to_chw, is_iterable, set_seed
class ImageRangeNormalizer(object):
""" divides input by 255 if int """
def __call__(self, obj):
if obj.dtype=='int':
return obj/255
return obj
class NumpyToTenso... |
5ba13f38588c54a71aa326652612ec951ea71f483dac1638b02564f061f95e75 | Python | 8,510 | 299 | # 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... |
0d54fc3694fa49d31969236d4eed5c59b3fe11a2596489ea977ee5337b317ef2 | Python | 8,514 | 208 | """
Clean close particles in a STAR file
Input: - STAR file
- Minimum scale
Output: - A copy of input STAR file where some rows can be filtered
"""
__author__ = 'Antonio Martinez-Sanchez'
###### Global variables
import numpy as np
import pyseg as ps
####################################... |
93b9f68b2d724d2c5f362ffd33e186e2985befdd3bc81395f96c02df13d2511c | Python | 8,514 | 245 | #!/usr/bin/env python
#
#===- run-clang-tidy.py - Parallel clang-tidy runner ---------*- python -*--===#
#
# The LLVM Compiler Infrastructure
#
# This file is distributed under the University of Illinois Open Source
# License. See LICENSE.TXT for details.
#
#===--------------------------------------... |
35540ed250d1e1db1bf8ee5ff27336ee62e5222189e4f90b8365d336200cc56c | Python | 8,516 | 205 | from collections import OrderedDict
import csv
from typing import List, Optional, Union
import os
import numpy as np
from tqdm import tqdm
from torch.utils.tensorboard import SummaryWriter
from .predict import predict
from chemprop.args import PredictArgs, TrainArgs
from chemprop.data import get_data, get_data... |
809b4d4e13509a5b034ad3100f4fccd6d7dd7d651b6f98c9be1cd9d74a3a5a82 | Python | 8,517 | 212 | """
Generates subvolumes and a segmentation mask for lumminal and shell regions for
every microtubule (the difference with previous versions is that this one allows the
further direct particle reconstruction within pymtubes package)
Input: - STAR file with the next columns:
+ CSV (fil... |
b0f3d266ad9ca6ef3a93caf07e8f583dc26dba9061de261c9e705fecb3fe236e | Python | 8,518 | 254 | # -*- coding: utf-8 -*-
import sys
import numpy as np
import pandas as pd
from scipy import sparse
def get_largest_component(func):
"""Decorator that extracts the largest connected component and
ensures the adjacency matrix is symmetric and binary."""
def wrapper(*args, **kwargs):
net, community... |
aa1a941995134c7a8061adcd51af23622c39c1ac84e0e5602f52defc2bca3974 | Python | 8,520 | 257 | #
# 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,... |
3d92d5e1e85ca3132e73ea82c483e279174c6276bac030905204b979eb373932 | Python | 8,521 | 199 | from .utils import get_dataframe, get_classes_labels, train_test_split
import random
import imageio
import numpy as np
import albumentations as A
import matplotlib.pyplot as plt
from tensorflow.keras.utils import Sequence, to_categorical
def train_augmentations(percent_resize=0.25):
"""
Train augmentations.
... |
804427b92713bd852e63a0227ff4550309bdeeea03163961387e71eeebbca802 | Python | 8,521 | 131 | # -*- coding: utf-8 -*-
OPTIMAL = False
CONFIGS = [
# add_lm_lazy_greedy
(114, ["--evaluator", "hadd=add(transform=H_COST_TRANSFORM)",
"--evaluator",
"hlm=lmcount(lm_rhw(reasonable_orders=true),transform=adapt_costs(plusone))", "--search",
"lazy_greedy([hadd,hlm],preferred=[hadd,hlm... |
da5a1c917688829514e5fe0f13ee6e53934000d1a1cee90e48ca8d931842f4de | Python | 8,524 | 217 | from __future__ import print_function, division
import numpy as np
import time
from collections import Counter
from pybullet_tools.utils import elapsed_time
from learn_tools.active_learner import ActiveLearner, format_x, THRESHOLD, tail_confidence
from learn_tools.learner import rescale, DEFAULT_INTERVAL, TRANSFER_W... |
57eac1c9558ba7f13790dc4045cd70a6f044d077628557d3b3a9ac10f0812180 | Python | 8,525 | 256 | import torch.nn as nn
import torch
import math
# from train_Customadc_noise import BITNUM
ADCBITNUMBER=5
BITNUM_SIG=ADCBITNUMBER
POINTNUMS=2**BITNUM_SIG
print('adc bit number=',BITNUM_SIG)
BITNUM_TANH=ADCBITNUMBER
POINTNUMT=2**(BITNUM_TANH-1)
noise_std=int(5)
print('WEIGHT_NOISE',noise_std)
def ramp_sigmoid_generati... |
1b35dc44ef21fc1028c15b29dc9c1a595bd2529e9090747f9a423db9f06a1937 | Python | 8,526 | 209 | import numpy as np
from scipy.sparse import csr_matrix
import networkx as nx
from rdkit import Chem
from collections import defaultdict
# feature dim
ATOM_DIM = 101
BOND_DIM = 11
FG_DIM = 73
FG_EDGE_DIM = ATOM_DIM
ALLOWABLE_BOND_FEATURES = {
'bond_type': ['SINGLE', 'DOUBLE', 'TRIPLE', 'AROMATIC'],
'conjugate... |
7606dc37b93720a0ecd6fd8a707dcc27f576ccf3c5ea1029ddf7dc19eb41bcc7 | Python | 8,527 | 308 | # 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... |
846a63c57cef0c5c3725d7036a50e278b8340c276f3eced8330f084438a88f22 | Python | 8,528 | 192 | from Pose_mdn_joint import Pose_mdn_joint
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 numpy as np
class Pose_multi_mdn_joint(Pose_mdn_joint):
def __init__(self,conf, name='deepnet... |
0454615fbef3e991a265c15e8c556e8534d90226e6ca31c168fe05d211df6d7f | Python | 8,531 | 210 | import numpy as np
from regtools.stitching.core.run_tissuecyte_stitching_classic import _visual_grid_cell
from regtools.stitching.core.tissue_montage import (
SectionTissueMask,
tile_mask,
apply_masked_flatfield,
TILE_SIZE,
)
def test_visual_grid_cell_even_column_is_top_down():
# Even c... |
680426f76eedaedba9b74d492510857c1f8237983675b7575192c50b981405c4 | Python | 8,532 | 257 | #!/usr/bin/env python3
"""
-------------------------------------------------------
getStimPoints.py Uses clean filter in vtk to extract
x,y,z coordinates of points with
a fixed inter-point distance.
The points are used as stimulation
... |
265355493b9c5b88bcb923bbd3daaa6f166bd355a7644deec90f3484171b6e9c | Python | 8,534 | 224 | """
Unified registration interface.
Provides method-agnostic wrappers for running registration and applying
transforms with either ANTs or Elastix backends.
"""
import os
import gc
from ..config import (
DEFAULT_REGISTRATION_METHOD,
HAS_ANTS,
C_WARN,
C_RESET,
)
from .ants import antsR... |
a787494da0aa28034ad8170b3477c00253d28f6dac867e4a09c3caf8e50ba5e6 | Python | 8,539 | 229 | # 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... |
cdd8f0e8176ecf9c91196153b123ec35a5776e1d80fb2d8f69c79f79d04f9c6e | Python | 8,539 | 190 | import copy
from monai.transforms import Transform, Compose
import numpy as np
import torch
from torch.nn.functional import grid_sample
from torch_geometric.data import Data
from torch_geometric.transforms import FaceToEdge
from gem_cnn.transform.gem_precomp import GemPrecomp
from gem_cnn.transform.simple_geometry impo... |
0b5964405cc4d9b5ef727dc266b0b2f4e5a22497acf115a2a616f5a7f2c128ab | Python | 8,540 | 231 | """
Created on Mon Dec 27 16:35:56 2021
@author: Haotian Teng
"""
import torch
import torchaudio
"""
This script train a VQ-VAE style embedding network on Nanopore sequencing signal.
@author: Haotian Teng
"""
import os
import sys
import torch
import argparse
import numpy as np
from typing import Union,List
from itert... |
55dbc13af73ed34858329f32323992b881e1116702ab1b817f4c0a114336e163 | Python | 8,543 | 216 | # -*- coding: utf-8 -*-
import os
from typing import Iterable, Union
import torch
from supar.config import Config
from supar.models.dep.biaffine.parser import BiaffineDependencyParser
from supar.models.dep.biaffine.transform import CoNLL
from supar.models.dep.crf2o.model import CRF2oDependencyModel
from supar.structs... |
981c96978400a11b3bd0ea71560e78e86345c0936aa5ed6d77eefcffbf51e8ee | Python | 8,543 | 228 | import torch
from torch import nn
from torch.nn import functional as F
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.math_operations.math_operations import MathOperations
from elasticai.creator.nn.integer.pointconv1dbn.design import (
PointConv... |
2aa63534b2ea247d5f05c5607732cf777e9aae15130becc5d64b564e6be90eb0 | Python | 8,544 | 259 | # -*- coding: utf-8 -*-
#
# Syncopy PSTH frontend
#
import numpy as np
from copy import deepcopy
import logging
import platform
# Syncopy imports
import syncopy as spy
from syncopy.shared.parsers import data_parser, scalar_parser, array_parser
from syncopy.shared.tools import get_defaults, get_frontend_cfg
from synco... |
87e4e965b3598d8e31c5e06f3aeb27907ce03f30de8275cf1f539e519ba2c1ec | Python | 8,544 | 231 | ################################################################################################################
# torch profiling adapted from https://github.com/pytorch/pytorch/blob/master/torch/utils/bottleneck/__main__.py
###
import torch
import cProfile
import pstats
import sys
from torch.autograd import profiler... |
d69deaa97d8d5a74e091279929a1665d1b42194c0518fe0ec4ff31678f133a7b | Python | 8,544 | 275 | # -*- coding: utf-8 -*-
"""
Created on Thu Dec 8 16:09:31 2022
@author: Dustin Garner
"""
import numpy as np
import pandas as pd
from scipy.spatial import Delaunay
import flycode.readfiles as readfiles
region_dict = readfiles.import_regions()
def remove_autapses(df):
"""Takes in a synapse df and removes all... |
7859ebd6e89c7ad05cb46330c5b95d227da0c0f68e83385bffc390091ffc950a | Python | 8,545 | 273 | from math import ceil, log2
import cocotb
import pytest
from cocotb.clock import Clock
from cocotb.triggers import ClockCycles, ReadOnly, RisingEdge
from cocotb.types import LogicArray
from cocotb.utils import get_sim_time
import elasticai.creator_plugins.multipliers as multipliers
from elasticai.creator.arithmetic i... |
9492df02e2a2b95858bedb54b103a2ca49c340f6e0f9f94bf26b4518a912b6be | Python | 8,546 | 171 | # +
import torch
from transformers import get_constant_schedule_with_warmup
import numpy as np
from tqdm import tqdm
from math import ceil
from .evaluation_metrics import print_topl_statistics
from .losses import binary_crossentropy_2d
import pandas as pd
def trainModel(model,fileName,criterion,train_loader,val_loader... |
12da68629459ccf96063cf94c49adf794634387725b00caa210be59b3e745749 | Python | 8,547 | 244 | """
Script to analyse tuning curves for both controls and controls vs glyt2+cno.
Fit tuning curves and cluster putative neurons accordingly; used
b-spline to fit tuning curves (default angle).
Based on tc_fun from tc_module: function to calculate firing rate associated to each discrete
wvar value; uses load_data, spi... |
5cf868eb045b8aa8056f109a955743e7a13788339d5a61a556004e1f7e94f074 | Python | 8,548 | 484 | from __future__ import annotations
import numpy as np
from scipy import ndimage as ndi
from skimage.filters import threshold_otsu
# ======================================================================
# LABEL-MAP VALIDATION
# ======================================================================
def validate_ins... |
f5e53f5665d17c5c2a9ba395d37ec8f7393778c9c0f3d12c0ce6e9ddf5f68267 | Python | 8,548 | 204 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""生成 game/data/pools.json —— 脑-游戏接口的神经元池定义（索引为"组排序后"空间）。
数据来源（只读）：
vendor/snedea-flybrain/data/connectome.bin.gz 二进制连接组（原始索引 = neurons.csv.gz 行序）
vendor/snedea-flybrain/data/neurons.csv.gz root_id 列表，行序即原始索引
vendor/snedea-flybrain/data/coordinates.csv.gz ro... |
16df65b5b54a18aa97683cc16b4b1db32e3ebd235b0879bb4f5f31d919bbe7a5 | Python | 8,549 | 184 | import os
import pickle
import datetime
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
def save_scan_image(
env,
x_nm: float = 0,
y_nm: float = 0,
pixel: int = 128,
scan_mvoltage: float = 1000.0,
scan_speed: float = 500,
scan_len_nm: float = 10,
... |
e264558de56298d9487675d4914c49970905e7ee8ed32259b68562017b6984c5 | Python | 8,550 | 245 | from __future__ import annotations
from pathlib import Path
import numpy as np
import pytest
from ase.atoms import Atoms
from ase.build import bulk, molecule
from ase.calculators.emt import EMT
from ase.io import read
from numpy.testing import assert_allclose
from quacc.atoms.core import (
check_charge_and_spin,... |
5b4d48ec7d2f04a64a0a9892260d85c77c237622074ef3c7646278d76e227490 | Python | 8,551 | 224 | # -*- coding: utf-8 -*-
import os.path
from lab.environments import MaiaEnvironment
from lab.steps import Step
from downward.checkouts import Translator, Preprocessor, Planner
from downward.experiments import DownwardExperiment
from downward.reports.compare import CompareRevisionsReport
from downward.reports.scatter... |
8d2821b8296c75f379f56908289f053a2bb7c1c17d4cc2df0749a192a98dc009 | Python | 8,551 | 191 | #! /usr/bin/env python
from __future__ import print_function
from collections import defaultdict
import os
import subprocess
import sys
DIR = os.path.dirname(os.path.abspath(__file__))
REPO_BASE = os.path.dirname(os.path.dirname(DIR))
sys.path.insert(0, REPO_BASE)
from driver import returncodes
BENCHMARKS_DIR = os... |
b0759d72065e33b7c809f697ff1aff9f4b4ab9f1b3c50993f225d3443c9e9673 | Python | 8,551 | 350 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import textwrap
HELP = "Convert suite name to list of domains or tasks."
def suite_alternative_formulations():
return ['airport-adl', 'no-mprime', 'no-mystery']
def suite_ipc98_to_ipc04_adl():
return [
'assembly', 'miconic-fulladl', '... |
0a641489a168a729c7df5a4e2de94465a836db2725e428f3b95c69b4830d50ec | Python | 8,553 | 166 | import os,copy
import numpy as np
import h5py
import SimpleITK as sitk
from ..io import imAdjust, imTrimBlack, readH5, writeH5
class sitkTile2Volume:
# 1. estimate transformation between input volumes
# 2. warp one volume with the transformation
# xyz order
def __init__(self, tiles_data, getVolume, ali... |
ea0dc4bc719e1a8beecbdeb58caf63fd74f8e9245cea3c567e89e82bb9e702a7 | Python | 8,553 | 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... |
2dae0d54c5409794f93212d8fb2012b39ce1067067a4383f9a4cc65d0ba7e467 | Python | 8,555 | 228 | import torch
from torch import nn
from torch.nn import functional as F
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.math_operations.math_operations import MathOperations
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQP... |
d83a2c4b696a7d33ea20b075fd64dca89c628f0361424740e2df3a6c2ed8ea2c | Python | 8,556 | 220 | import os
import os.path
import warnings
from glob import glob
from typing import Any, Callable, Dict, Optional, Tuple
from urllib.error import URLError
import cv2
import numpy as np
import pandas as pd
import torch
import torch.utils.data
import torch.utils.data as data
from sklearn.model_selection import train_test_... |
5f0d9202d3c7172e2645650ee9a93063ae73e643099b52c71bd72dfa254621f6 | Python | 8,557 | 173 | import torch
from torch.utils.data import DataLoader
import numpy as np
from torch.autograd import Variable
import time
from src.Human.utils import normalize_range, un_normalize_range, check_cuda
from src.Human.src_nn.Dataset import Dataset
from src.Human.src_nn.Dataset import DatasetNOE
from src.Human.src_nn.Network ... |
a71ed1367fbe1f425b65dca166883a32105141ba18b4697b426909c255e47abc | Python | 8,557 | 195 | """
Script to run drug response classification experiments (sensitive/resistant)
for all chosen drugs with stratified train/test sets.
"""
import sys
import argparse
import itertools as it
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
import pancancer_evaluation.config as cfg
... |
b24bde93a6da00c0c76110c4aefdba0ad7f27291ccb2599ea4c4fb726edd18b8 | Python | 8,559 | 195 | """
Script to run pan-cancer classification experiments for all chosen combinations
of gene and cancer type.
"""
import sys
import argparse
import itertools as it
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
import pancancer_evaluation.config as cfg
from pancancer_evaluation.d... |
cf6ef967c27464b81a920215fb4a92168bcfb50ac72cd2aeccb5d082381408cd | Python | 8,560 | 250 | from collections.abc import Mapping
from enum import Enum
from functools import _find_impl, singledispatch
from types import MappingProxyType
from typing import Callable, Type, TypeVar
from warnings import warn
import numcodecs
import numpy as np
import pandas as pd
import zarr
from packaging import version
from panda... |
2204a742376889ad8d912551999db9fd355117786e0f7b1abb4e46a2de2ab918 | Python | 8,563 | 239 | #!/usr/bin/env python3
# coding: utf-8
import os
import os.path as osp
from pathlib import Path
import numpy as np
import argparse
import time
import logging
import torch
import torch.nn as nn
import torchvision.transforms as transforms
from torch.utils.data import DataLoader
import torch.backends.cudnn as cudnn
cudn... |
6245eacaa5ec5da9af14d0c0fbeaf7d2d767a3b6c0c3cd95d8b2d242d4d51b7c | Python | 8,563 | 284 | import os
import pickle
import bct
import numpy as np
import pingouin as pg
from scipy.stats import spearmanr, mannwhitneyu, iqr
import seaborn as sns
import matplotlib.pyplot as plt
import colorsys
from strength_preserving_rand_sa import strength_preserving_rand_sa
#general functions
def pickle_load(file):
r... |
44064acd8634875a5468586769028c990c2e2ca234593612443e4bbd00e1f7e3 | Python | 8,569 | 406 | #!/usr/bin/env python
# coding: utf-8
# In[ ]:
import sys
sys.path.append("../scripts")
# In[ ]:
import os
import Models_02 as models
import Paths as paths
import Preprocessing_01 as preprocessing
import pytorch_lightning as pl
import Utils_00 as utils
from monai.utils import set_determinism
from pytorch_lightn... |
efc4c6c43a258d0c3fed03a1dc21007f9168bc6478a8d48e76b1ed3cd69467e5 | Python | 8,571 | 280 | #!/usr/bin/env python
# coding: utf-8
# ## Apply an image-based profiling pipeline using pycytominer
#
# As described fully in [Caicedo et al. 2017](https://doi.org/10.1038/nmeth.4397), an image-based profiling pipeline consists of three core steps:
#
# 1. Aggregation
# 2. Normalization
# 3. Feature selection
#
# [... |
19ed657f0623cb161d3097617bef3a068e0ead39d97641e5e4663ad3b7a3ee56 | Python | 8,572 | 59 | import os
import random
import math
import sys
# Check if the required arguments are passed
if len(sys.argv) != 3:
print("Usage: python script.py [sweep|neutral] <num_replicates>")
sys.exit(1)
replicate_type = sys.argv[1]
num_replicates = int(sys.argv[2]) # Ensure num_replicates is an integer
... |
26d308b5af09b859025d54c7bd98669de004748327a6c757f389ce58a176e2b9 | Python | 8,572 | 280 | """distutils.archive_util
Utility functions for creating archive files (tarballs, zip files,
that sort of thing)."""
import os
from warnings import warn
import sys
try:
import zipfile
except ImportError:
zipfile = None
from .errors import DistutilsExecError
from .spawn import spawn
from .dir_util import mk... |
0361836a766eac612ad45e6677b27e3c5864280a91a9d21df04c1273db89dda0 | Python | 8,574 | 272 | # -*- coding: utf-8 -*-
#
# hybridLFPy documentation build configuration file, created by
# sphinx-quickstart on Wed Apr 11 11:19:04 2012.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... |
33e4b32053069944b99a97c0150af49927a17123cd52af9b760b1aed2c02c230 | Python | 8,584 | 266 | # 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... |
39e55921a9502e1a87abbc5bae5e228bc6daf7864e9632b07d474efff994bbf8 | Python | 8,588 | 284 | import operator
from collections.abc import Callable, Iterable, Sequence
from functools import reduce
from typing import Any, Protocol, TypeGuard, cast, overload
from elasticai.creator import ir
type ShapeTuple = tuple[int] | tuple[int, int] | tuple[int, int, int]
def is_shape_tuple(values) -> TypeGuard[ShapeTuple]... |
e744028e49070f1c5e966d483734a16a516d82898aed953051aa5100680a2203 | Python | 8,588 | 222 | """PointCloud-tracking smoke tests for transform_input_points.
The function depends on a fully-formed registration output directory (ANTs
transforms, axis alignment, optional Laplacian field). These tests mock
the ANTs and Laplacian backends with identity transforms so they run
quickly without external binaries.... |
0e26e48c601ef91a247283bdd5523922fd3a367c29a69f6bf251e0b22c484334 | Python | 8,589 | 243 | import copy
import logging
import numpy as np
import os
import time
from threading import Thread
from queue import Queue
from queue import Empty
import carla
from srunner.scenariomanager.carla_data_provider import CarlaDataProvider
from srunner.scenariomanager.timer import GameTime
def threaded(fn):
def wrapper... |
b6e9b46a08ef3f8a6e1fdbf17aec2525b986c2ee61e8448981e5ef61086c2abd | Python | 8,590 | 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... |
8d7619069034e32513b95c615f92dc358162a7abef908c5eb1aba97093c597e7 | Python | 8,591 | 214 | # 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... |
9a835ea51f8630c9638bc4e03caf57a1988fefd1a9c601270f7ee82bcf66e928 | Python | 8,594 | 212 | #!/usr/bin/env python2.7
from __future__ import print_function
from random import uniform
from pddlstream.algorithms.search import solve_from_pddl
from pddlstream.utils import read_pddl, irange, INF, randomize, Profiler
from pddlstream.language.constants import get_length, PDDLProblem, print_solution, Exists, And, N... |
2b9ba3723121f969da554d212e780171a59a9989f447df5c11e72b643cdbadf9 | Python | 8,595 | 249 | import numpy as np
import pandas as pd
import h5py
import json
import re
import os
from mne_bids import BIDSPath
from mne_bids.write import (
_participants_tsv,
_participants_json,
make_dataset_description
)
import argparse
SOURCE_DIR = 'logs'
BIDS_ROOT = 'bids_dataset'
DELAY_SAMPLES = 3
_stringify = lamb... |
6934bad43cb274c518394ed06f6dad89b849d90358f02bb8ec41481fb12dec35 | Python | 8,595 | 267 | import pandas as pd
import numpy as np
from tqdm import tqdm
import pickle
import joblib, os
from joblib import Parallel, delayed
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset, DataLoader
import torch
from torch import nn
from . import utils
class MultiDS(Dataset):
def ... |
5d43b9661c2424093c761d90a49e01498c3f467b4d64386b963b9cbed5af683c | Python | 8,597 | 188 | from typing import Any, Callable, Dict, Tuple, Union
import pandas as pd
import mne
import numpy as np
import os
from .base_dataset import BaseDataset
from ...utils import get_random_dir_path
def default_read_fn(file_path, **kwargs):
# Load EEG file
raw = mne.io.read_raw(file_path)
# Convert raw to epoch... |
dd59f1040756936c5c909f261706b3f76b755cfb0147a477bea1bc740c2f46c3 | Python | 8,597 | 219 | """
Script to train pan-cancer mutation classification models using NN.
"""
import sys
import argparse
import itertools as it
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
import pancancer_evaluation.config as cfg
from pancancer_evaluation.data_models.tcga_data_model import TCG... |
db2e76d832f32816e8b8ec83f3f3dde4438d13449ccfbc2f31e4636f32ba09a8 | Python | 8,598 | 237 | import pytest
import numpy as np
import pandas as pd
import seaborn as sns
import statsmodels.formula.api as lme
from pyrelimri.similarity import image_similarity
from pyrelimri.tetrachoric_correlation import tetrachoric_corr
from pyrelimri.icc import sumsq_icc
from hypothesis import given, strategies as st
from hypoth... |
d064913235e7972f0a06db647725a1dd7fadbd78f64d9712ff77c810a0d2e567 | Python | 8,599 | 229 | import lightning.pytorch as pl
import torch.nn as nn
import torch
import math
import matplotlib.pyplot as plt
import matplotlib
from torchmetrics.regression import MeanAbsoluteError, MeanAbsolutePercentageError, MeanSquaredError, R2Score, PearsonCorrCoef
from torchmetrics import MetricCollection
import os
#starts_to_lo... |
8b7ae1714c8e66d12ea94581775ae15db6c6926b9030a77b33d5b74fab83c436 | Python | 8,600 | 247 | # encoding: utf-8
import _init_paths
import fire
import time
import pandas as pd
import os
import numpy as np
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision
import torch.nn.functional as F
from tqdm import tqdm
from collections import OrderedDict
from torchvision import da... |
def0ca706c4e03b97c8b4be9dfe641dc976cf6d7aa614f3e2802cfab1a2e93c5 | Python | 8,601 | 207 | # 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... |
db83167b0493c4f01fe69b29c523c8916e6ae39eb75893bd0f0215046d2b4dc8 | Python | 8,602 | 203 | from collections import deque, Counter
from pddlstream.algorithms.reorder import get_partial_orders
from pddlstream.language.constants import is_plan
from pddlstream.language.conversion import substitute_expression
from pddlstream.language.function import FunctionResult
from pddlstream.language.optimizer import get_cl... |
288a66d59d8cde6b34f17101267ef302a2d608ba08b086f699c28b295457b15b | Python | 8,603 | 206 | from typing import List
from typing import Union
import numpy as np
from skimage import transform
from skimage import feature
import cv2
from merlin.core import analysistask
from merlin.util import aberration
class Warp(analysistask.ParallelAnalysisTask):
"""
An abstract class for warping a set of images so... |
3b99706caa9ec098b2776979d26d12eed0c1ddb0a1ba879c3531a0064582f996 | Python | 8,604 | 217 | # Node-group asset "Symmetry Helical" (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 impor... |
a112c24ce73fa4a630d775ebeb36571586a69edc006d95a94b34042709c620d3 | Python | 8,605 | 251 | # 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... |
d419aad7b110534195029b0f7448d2d0f7b4898f15344e770bbbab43df15e625 | Python | 8,607 | 267 | # 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... |
7356a8a65efd729f30b6ece160ba17126db770fcadabbd9e3665eab336f9ffd0 | Python | 8,610 | 212 | # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/02_utils.ipynb.
# %% auto 0
__all__ = ['group_extract', 'sample', 'to_np', 'generate_steps', 'set_seeds', 'config_hold_out', 'config_criterion',
'get_groups_from_df', 'get_cell_types_from_df', 'get_sample_n_from_df', 'get_times_from_groups']
# %% ../nbs/02... |
aa7207e267b016ccdc79a5cab3f390a30fd06e2d083050ab893415bdd7d2e4df | Python | 8,610 | 270 | # 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... |
d4bb2468bf24350bb92df17b2796cc173ebc38a4b80a959805dbb5c3d55da986 | Python | 8,610 | 269 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import json
import math
import anndata
import scipy
import scanpy as sc
import os
# %%
import sys
import numpy as np
import pandas as pd
from tqdm import tqdm
import pickle
import matplotlib.pyplot ... |
e72b51a0fc84884beab484fe423c2c643e1572a710551f0e66ce174482767fe5 | Python | 8,610 | 262 | """
Set of functions for generating DevCCF to CCFv3 mappings as a Sankey flow diagram
Used to generate Fig 5c
"""
import nrrd, json
import SimpleITK as sitk
import numpy as np
import pandas as pd
from anytree import Node
import plotly.graph_objects as go
def read_metadata_excel(metadata_filename):
dtype_ty... |
a587d24204635504dca82c79533b2f545d8d0f2c5c3855ee1f65a0e2850d0359 | Python | 8,611 | 264 | #!/usr/bin/env python3
import argparse
import logging
import os
import shutil
import sys
from pathlib import Path
import pandas as pd
from Bio import SeqIO
from Bio.Blast.Applications import NcbiblastnCommandline, NcbimakeblastdbCommandline
from viper_clustering import viper_utilities as vu
def parse_arguments():
... |
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