sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
c52a0d6b65b9cdff8986d36fd2350ca9078d527b4de17d3bdfe94a98d62a35a9 | Python | 3,193 | 94 | """
Script to convert soccertrack dataset format to YOLOv5 format.
"""
import argparse
from pathlib import Path
from joblib import Parallel, delayed
import cv2
import numpy as np
import yaml
import soccertrack
from soccertrack import Camera
from soccertrack.logging import logger, tqdm
# Move each file to their resp... |
45a0b9804717dbc617cd846cd5d0d90140f2a09a33f372abc0312755c5629df6 | Python | 3,195 | 89 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os
import os.path as osp
import tempfile
import zipfile
import mmcv
from mmengine.utils import mkdir_or_exist
CHASE_DB1_LEN = 28 * 3
TRAINING_LEN = 60
def parse_args():
parser = argparse.ArgumentParser(
description='Convert CHASE_DB1... |
a451a932c3dd5a91045855708ddf9f4fa1382e4bc73bac53e2b11fe97330af12 | Python | 3,196 | 90 | # coding=utf-8
# Copyleft 2019 Project LXRT
import os
import os.path as osp
import sys
import csv
import base64
import time
from tqdm import tqdm
import numpy as np
import json
import pickle
import pdb
csv.field_size_limit(sys.maxsize)
FIELDNAMES = ["img_id", "img_h", "img_w", "objects_id", "objects_conf",
... |
d109abbc95164bb3da2fb77a46fb33102c83b06a300728ecd5712c633d8f819f | Python | 3,197 | 100 | """Floor geometry with grid and shadows support."""
import typing as t
from pydantic import Field, field_validator
from .base import BaseGeometry
class Floor(BaseGeometry):
"""A floor plane with grid and shadows support."""
active: bool = Field(
default=False,
description=(
"Wh... |
587421edef9464521fc28aecb3eb03231a3ba84432eb2b5f9257501a3009f9d0 | Python | 3,198 | 90 | from __future__ import print_function
import pytest
import time
import random
from keras.datasets import cifar10
from keras.datasets import cifar100
from keras.datasets import reuters
from keras.datasets import imdb
from keras.datasets import mnist
from keras.datasets import boston_housing
from keras.datasets import fa... |
15cb425f2d27f848ad2d008ec2ed6aae3d17bf443505b34fdf33f24fc3d87ee8 | Python | 3,201 | 116 | # -*- coding: utf-8 -*-
"""
Some functions comes from
https://github.com/scilus/scilpy/blob/master/scilpy/io/utils.py
"""
import glob
import os
def add_overwrite_arg(parser):
"""
Add overwrite option to the parser.
Parameters
----------
parser: argparse.ArgumentParser object
"""
parser.a... |
f383f40a880a60637f111a1f8066b954c726367a919eb189c3ba205d24d1959d | Python | 3,202 | 105 | # Residual Dense Network for Image Super-Resolution
# https://arxiv.org/abs/1802.08797
from model import common
import torch
import torch.nn as nn
def make_model(args, parent=False):
return RDN(args)
class RDB_Conv(nn.Module):
def __init__(self, inChannels, growRate, kSize=3):
super(RDB_Conv, self)... |
4a4d5d50e3cf0c531457d29ae425b3a5ff63fea46fd540b7df63f012b8895e85 | Python | 3,204 | 87 | # 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
#
# http://w... |
ba971c714e3b4f1e109665b9fa8170d8261733fc0132f4ed4979586637151089 | Python | 3,205 | 96 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 9 15:24:53 2021
@author: Engi
"""
import os
import platform
platform.system()
# define starting datafolder
if platform.system() == 'Darwin':
os.chdir('/Volumes/BBC/BBC/WP1/data/EEG/tsk')
base_datafolder = '/Volumes/Elements/'
else:
os.... |
b76fcdf45e25889410747dc18031f25e9db750cdaa5923762b5c433099f25438 | Python | 3,206 | 109 | #!/usr/bin/env python
"""
MetaWIBELE: filter_clusters module
Filter out specific clusters
Copyright (c) 2019 Harvard School of Public Health
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 witho... |
d3ec528e5a641ee4dec54eb56aa6c7970187d4de4b6cb93055a4c191050fe468 | Python | 3,208 | 106 | """Tests for CLI bookmarks commands."""
from __future__ import annotations
from typing import TYPE_CHECKING
from zndraw.schemas import BookmarksResponse, StatusResponse
from .conftest import invoke_cli
if TYPE_CHECKING:
from typer.testing import CliRunner
def test_bookmarks_list_empty(
cli_runner: CliRun... |
654188dc506f2d2a39889813be1ca87d491f46adf15589000fdbf86de7500431 | Python | 3,209 | 100 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmseg.models.backbones.swin import SwinBlock, SwinTransformer
def test_swin_block():
# test SwinBlock structure and forward
block = SwinBlock(embed_dims=32, num_heads=4, feedforward_channels=128)
assert block.ffn.embed_dims =... |
8c874cf39ba03eb9b968f33b3b4f47f01e927fc688aaa38100849b3848dfc213 | Python | 3,209 | 126 | import numpy as np
import nearl.all_actions as all_actions
# from nearl import features
agg_map = {
1: "mean",
2: "std",
3: "median",
4: "variance",
5: "max",
6: "min",
7: "sum",
8: "slope"
}
def get_mean(points):
return np.mean(points)
def get_std(points):
return np.std(points)
def get_med... |
05b0cdc85a5e185b66a5225102208f69920c8e80a0fc329b58c11a4ad092b88e | Python | 3,210 | 107 | """
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 numpy as np
import pytest
import torch
from ocpmodels.modules.evaluator import (
Evaluator,
cosine_similarity,
magnitude_... |
0e95cc1433b9e239dbc51fbcc5f6561702ebbb0fec101dbbfa882c068ae1139c | Python | 3,212 | 118 | import pytest
from medperf.exceptions import CleanExit
from medperf.commands.mlcube.delete_keys import DeleteKeys
from medperf.tests.mocks.encrypted_key import TestEncryptedKey
PATCH_DELETEKEYS = "medperf.commands.mlcube.delete_keys.{}"
CONTAINER_ID = 1
@pytest.fixture
def deletekeys(mocker):
mocker.patch(
... |
c117570ee6fb143500171e1c7f516326c455c791b093236bd4cc7948f06f6f44 | Python | 3,212 | 91 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import glob
import os.path as osp
from mmengine import Config
from mmengine.fileio import dump, load
def parse_args():
parser = argparse.ArgumentParser(
description='Gather benchmarked model evaluation results')
parser.add_argument('conf... |
25bc7189ab234653f3af2eb47aeab1992c0d72b35589c543c774fd95c43103aa | Python | 3,213 | 70 | # Top 20 color words in English
color_words = ['red', 'green', 'blue',
'yellow', 'pink', 'black',
'white', 'gray', 'purple',
'orange', 'brown', 'beige',
'gold', 'silver', 'navy',
'teal', 'olive', 'maroon',
'violet', 'cyan']
... |
b8e887fa0328bdf157739f5adec060d755a12d4919fdd7d3d832fd505525e665 | Python | 3,213 | 102 | """Unit tests for broadcast_room_update helper routing logic.
These tests cover the scoped delivery introduced in Task 18:
- PUBLIC rooms broadcast to the shared rooms:feed channel.
- GROUP rooms fan out to each group member's user:{uid} channel.
- PRIVATE rooms deliver only to the owner's user:{uid} channel.
Real so... |
01557cde38a9da2924e04afdd5610236e193c68494353fd39bd4bebccd9945ae | Python | 3,214 | 96 | import argparse
import os
import re
import yaml
import json
import pandas as pd
import SimpleITK as sitk
def convert_to_brats_label_style(tool_outputs_dict):
output_folder = "/corrected_predictions"
os.makedirs(output_folder, exist_ok=True)
tool_outputs_dict_corrected = {}
for subj, path in tool_outpu... |
19e53e591e82ddf6e5a91adf506ee1c4af741372de0cd9fe003c12f4643cab38 | Python | 3,218 | 98 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Tests the h5py._hl.filters module.
"""
impo... |
383cae47127e1aa4912850b396d3d23d116ee52b05e3410207b76f8e10ddbbb0 | Python | 3,219 | 74 | import numpy as np
import pytest
from guppy.analysis.cross_correlation import compute_cross_correlation
def test_identical_arrays_max_correlation_at_lag_zero():
signal = np.sin(np.linspace(0, 4 * np.pi, 200))
result = compute_cross_correlation([signal], [signal], sample_rate=20.0)
cross_corr_row = result... |
27539bf9e8722c72787d765309f0af8407fafeffe8ace3125d02ac04f4384a7e | Python | 3,221 | 91 | import socket
from dataclasses import asdict
import numpy as np
import pytest
import xgboost as xgb
from xgboost import RabitTracker, build_info, federated
from xgboost import testing as tm
from xgboost.collective import Config
def run_rabit_worker(rabit_env: dict, world_size: int) -> int:
with xgb.collective.C... |
6040c2c8d2dede8fae5272454ef04229e9d8686eb14b391438b3bd9dfd18b530 | Python | 3,224 | 136 | import os
from medperf.exceptions import ExecutionError
import pytest
from medperf.tests.mocks.dataset import TestDataset
from medperf.commands.dataset.export_dataset import ExportDataset
PATCH_EXPORT = "medperf.commands.dataset.export_dataset.{}"
@pytest.fixture
def dataset(mocker):
dset = TestDataset(id=None... |
91cce944b3ac55effc12608bfdd30789ba5c9aa73beaf3c7deb629e2f2fa5503 | Python | 3,224 | 74 | import numpy as np
from guppy.utils.artifact_windows import (
complement_windows,
coords_to_windows,
merge_windows,
windows_to_coords,
)
class TestMergeWindows:
def test_disjoint_windows_are_sorted_and_unchanged(self):
assert merge_windows(windows=[(5.0, 6.0), (1.0, 2.0)]) == [(1.0, 2.0),... |
abe1d4cb9461989bd510730fb18443a362104da1597a06c647b412c32306bd16 | Python | 3,225 | 72 | # For benchmark preprocessing usage:
#
# python Preprocessing_scFile.py --inputfile /home/wangjue/biodata/scData/allBench/9.Chung/T2000_UsingOriginalMatrix/T2000_expression.txt --outputfile /home/wangjue/biodata/scData/9.Chung.csv --cellcount 317 --genecount 2000 --split space --cellheadflag False
# python Preprocessin... |
2d0b78827495ebb06d551d9900cf0674342c4b0dd0ec1178bcc1b46a8328746b | Python | 3,227 | 109 | from typing import Optional
from medperf.entities.aggregator import Aggregator
import typer
import medperf.config as config
from medperf.decorators import clean_except
from medperf.commands.aggregator.submit import SubmitAggregator
from medperf.commands.aggregator.run import StartAggregator
from medperf.commands.list... |
ec7cf686ebe7fc6150ad2726d7a3df3b1e06ec08b7b6b8299d05b4683ec82440 | Python | 3,227 | 100 | """
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 logging
import os
from ocpmodels.common.registry import registry
from ocpmodels.trainers.forces_trainer import ForcesTrainer
class ... |
d40b7fffc94da8e9833d1206ded70c493b6f0e6beae589543c72d80f9b3185c5 | Python | 3,228 | 112 | from .token_storage import TokenStore
from medperf.config_management import read_config, write_config
from medperf import config
from medperf.exceptions import AuthenticationError
from medperf.entities.user import User
def read_user_account():
config_p = read_config()
if config.credentials_keyword not in conf... |
e1bdeb3b36afc905be23aad6bf0a2984c61ab557d221b1038d597ca9ac604427 | Python | 3,228 | 84 | import numpy as np
import pytest
from dante.obj_functions import Ackley, Rastrigin, Rosenbrock, Griewank, Michalewicz, Schwefel
class TestFunctions:
@pytest.mark.parametrize(
argnames=("dims", "x", "expected", "scaled_expected"),
argvalues=[
(3, [1, 2, 3], 7.016453, 14.231930),
... |
ddfcbcf2f61f111ef93f184ae496f4113b7fea104a4ba16688e88224fa51f8aa | Python | 3,229 | 97 | """
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 sympy as sym
import torch
from torch_geometric.nn.models.schnet import GaussianSmearing
from ocpmodels.common.typing import assert_is... |
d367c12b09f12755cdcfcec2c0d0c7c03daddd1e7d195cdd118b60c9ce1f8853 | Python | 3,230 | 104 | #!/usr/bin/env python3
"""Smoke-check a downloaded eggnog-mapper data dir.
Verifies that:
- eggnog.db exists, is a v7 schema, has the expected core tables
- prots and protein_names have plausible row counts
- taxa.db is reachable and has a species table
- eggnog_proteins.dmnd is present (basic byte-level sanit... |
f4ab54bd787739adef0a1afbe9877ca81763b9a5ea844f5253658f2d297c4213 | Python | 3,231 | 104 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 25 12:02:59 2024
@author: AC
"""
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.linear_model import SGDClassifier
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix, roc_a... |
572f7b3b2ab27f9618d6451b13d7ee9478e171583d29cf145e29e0b53e9402c5 | Python | 3,232 | 93 | ##
import bz2
import gzip
import os
import re
import sys
CLEAN_SEQ = re.compile("[\s\-\.]+")
def _fasta_open(source):
"""Open a FASTA source for text reading, auto-detecting gzip/bzip2."""
from pathlib import Path
if not (os.path.isfile(source) or Path(source).is_file()):
return iter(source.split... |
d1fe42f45c30aa2e855e7ecc9ae40f48860c53346d688a7febccdbbc569912c7 | Python | 3,232 | 88 | # Dynamic features: property density flow and marching observers
################################################################
import h5py
import nearl
import nearl.features
import nearl.featurizer
import nearl.io
FEATURIZER_PARMS = {
"dimensions": 32, # Dimension of the 3D grid
"lengths": 16, # Length ... |
ec71e431ed24ed5e0410efc76502d3bd581e23e97fa72678b86dec880a968f1d | Python | 3,232 | 80 | """Mixin of contract tests for :mod:`guppy.utils.dandi_filter`.
Bound twice: once in ``test_dandi_filter.py`` against a local server that answers byte ranges as
the archive does, serving real NWB files, and once in ``test_dandi_filter_live.py`` against the
archive itself. The offline binding is a faithful substitute f... |
9ca7e3b47a8214f0108bc02c9d50ec1b209a86556fb97fb7d6abf52627f7d013 | Python | 3,234 | 80 | from qtools.relative_relevance.utils import get_non_zero_features_and_positions, find_folders_with_subfolder, is_larger_subtree, merge_runs_by_epoch, create_df_every_fifth
from qtools.relative_relevance.visualize import plot_relative_relevance, plot_delta_relevance_boxplot
import numpy as np
from scipy.stats import ma... |
d232006c0d33cfa4783d8bf2cb85a10fc4a481137c52ba453c41e3c599e401da | Python | 3,236 | 109 | from typing import Callable, Dict, Optional, Type
import torch
from .blocks import (
AgnosticNonlinearInteractionBlock,
AgnosticResidualNonlinearInteractionBlock,
AtomicEnergiesBlock,
EquivariantProductBasisBlock,
InteractionBlock,
LinearDipoleReadoutBlock,
LinearNodeEmbeddingBlock,
Li... |
7b0d178dbfae5999cf6aad477a2867eb23275a758b69693b27f7be7c955633ea | Python | 3,240 | 95 | """
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 sympy as sym
import torch
from torch_geometric.nn.models.schnet import GaussianSmearing
from .basis_utils import real_sph_... |
776d184fb16fd6924fec5cff3755d3642422f362a34755c2a78280bba43a1dd5 | Python | 3,242 | 81 | import ants
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
import scipy
import imageio
from skimage.color import rgb2gray
from scipy.ndimage import affine_transform
import cv2
from glob import glob
def calculate_affine(srcPoints, dstPoints):
# Add a fourth coordinate of 1 to each point
... |
9bbbe42cfa8ab2c57709d6f536eb83e6d7e12817b90d6e16afcb6e26ae3bf3f6 | Python | 3,243 | 106 | """Window algebra for artifact removal.
The Select Artifact Windows page asks the user to mark the periods where
*artifacts occurred*, but ``coordsForPreProcessing_<recording_site>.npy`` stores
the periods to *keep*. The conversion between the two lives here so it is
testable independently of the Panel page.
"""
impo... |
becdab8bbbb7405057e1527c34259ee78b5337df2791387079e537ca3844f67b | Python | 3,243 | 100 | """Utility functions for graphs."""
from typing import List, Optional
import numpy as np
import torch
from torch import Tensor
def get_edges_index(
combined_mask: Tensor,
pos: Optional[Tensor] = None,
edge_cutoff: Optional[float] = None,
remove_self_edge: bool = False,
) -> Tensor:
r"""
Args... |
a46c104dd1f017da57ca4186f2564767224a533e9a0bf7b6371942e819e85fa2 | Python | 3,244 | 90 | #!/usr/bin/env python3
#
# Calculates statistics about the means reported in the midpoints data.
#
import numpy as np
import base
nooocytes = True
qand = ' and cell != "Oocyte" group by pub'
# Query db
with base.connect() as con:
c = con.cursor()
def g(x):
q = f'select {x} from midpoints_wt where {x}... |
4a3e4366a99ec5a647c503d50feab67c6705fb7ccc52c695bc0419218962c458 | Python | 3,245 | 115 | import numpy as np
import json
import os
# import gym
import gymnasium as gym
############################### Define the functions ###############################
class LunarLander:
def __init__(self, dims=100, turn=1):
self.dims = dims
self.lb = 0 * np.ones(self.dims)
... |
70c87e0d4da10485a5734689a7ed80aa1075cb7aaf4512d687daeefa5e97478f | Python | 3,245 | 94 | import os
import pandas as pd
from sklearn.preprocessing import StandardScaler
DATA_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), '../CSV/Data')
def preprocess_data(df, drop_cols_range, target_col='Permeability'):
"""
Prepares feature and target datasets.
Parameters:
- df (pd.DataF... |
117b88abe60c1d8cd425c43bd7addb36091e2d60939e2b1787601ea59b24a09b | Python | 3,246 | 113 | from copy import deepcopy
import typer
from medperf import config
from medperf.decorators import configurable, clean_except
from medperf.utils import dict_pretty_print
from medperf.config_management import read_config, write_config
from medperf.exceptions import InvalidArgumentError
from medperf.commands.utils import ... |
6be092e5492b73a6b42112cb13c5ea3dce3c099b40db677253fa60673887dfaa | Python | 3,246 | 77 | # 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
#
# http://w... |
cd69cb6bddcb2a163df3cfce173f400da5eb4ae8043c3f99dad325ce2be8dac9 | Python | 3,246 | 89 | # 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
#
# http://w... |
4f41d4656d2680bac74eeceecc04698c6b29ea0d7948e9e97e2bdf6e77c17658 | Python | 3,247 | 89 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from scipy import stats
import os
from global_setting import *
#################### Hyperparameters ####################
mouse_name = 'S'
day = 'day1'
module = '1'
session = 'open_field_1'
# cell_id_list = [38, 7, 157, 12, 20, 14... |
9885c43d3e7a8d29b13bc52cc0d570d6ee29f0b47e6ac175e93cd62d4b7d4048 | Python | 3,247 | 65 | # Copyright (c) OpenMMLab. All rights reserved.
# yapf: disable
from .ade import ADE20KDataset
from .basesegdataset import BaseCDDataset, BaseSegDataset
from .bdd100k import BDD100KDataset
from .chase_db1 import ChaseDB1Dataset
from .cityscapes import CityscapesDataset
from .coco_stuff import COCOStuffDataset
from .dar... |
da056e7c386dfbdf7964c832cf385f9fcca8bdfa88345fb38b03e57fdfc62f90 | Python | 3,247 | 95 | """
Demo for using `process_type` with `prune` and `refresh`
========================================================
Modifying existing trees is not a well established use for XGBoost, so feel free to
experiment.
"""
import numpy as np
from sklearn.datasets import fetch_california_housing
import xgboost as xgb
d... |
101d56a85f2896881f1f0ad991d59b9d36256084d45142be80ee3d3dce5f0ba4 | Python | 3,248 | 107 | """Isosurface geometry for volumetric data visualization."""
from typing import Self
from pydantic import BaseModel, ConfigDict, Field, model_validator
class Isosurface(BaseModel):
"""An isosurface extracted from a 3D volumetric grid.
References a key in ``atoms.info`` that contains a dict with:
- ``gr... |
83f353d8d4aa0eb88f133aa430cfa78306379b606d4f4a149f453133a4b45eec | Python | 3,249 | 90 | import numpy as np
class ReinforcementLearning:
def __init__(self, num_states, num_actions, learning_rate=0.05, discount_factor=0.95, epsilon=0.05):
"""
Initialize the reinforcement learning module with explicit state and action value functions.
Args:
num_states: The number of p... |
fefdcd5d8cedfb6a16742da1c303635702fa4d039ab11f9d9ef7d1ceecf780e9 | Python | 3,250 | 119 | """
U-NET 3D IMPLEMENTATION
"""
import torch
import torch.nn as nn
class ConvBlock(nn.Module):
def __init__(self, in_channels, out_channels):
super().__init__()
self.conv1 = nn.Conv3d(in_channels, out_channels, kernel_size=3, padding='same', padding_mode='reflect')
self.conv2 = nn.Conv3d... |
1096f5dfc51838d99d5a68a52f1221ea3bed0e7edeb73c55811c3c0a9b0112f8 | Python | 3,253 | 89 | import os
import glob
data_path = "/Users/Gregg/Dropbox (MIT)/2021 Gregg rotation/Katya_data/BM019_longitidunal_good_examples/p28/Cell7/Dend2"#"/Users/Gregg/Dropbox (MIT)/2021 Gregg rotation/kyle_data/ASC27/Cell01/ASC27_cell01_a1-5_tseries-018"#r"/Users/Gregg/Dropbox (MIT)/2021 Gregg rotation/kyle_data"
collect_summa... |
4b25e606abf7dd835cc7e96f275826709ae2eeb525bef9ce60bf29693c20b370 | Python | 3,255 | 122 | """
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 math
from typing import Optional
import torch
from ..initializers import he_orthogonal_init
class Dense(torch.nn.Module):
"""
... |
658154a91155d1e03dbc2be699574e22e8c6a26f1d477b0015f8b245746b69ce | Python | 3,255 | 96 | # -*- coding: utf-8 -*-
"""
Created on Thu May 16 19:47:10 2024
@author: mbmad
"""
from patchanalysis.measures.measuretools import NoResultError, InvalidRecordingError, \
withinEachSweep, withinEachSweepHzXuYuCu
from patchanalysis import TimeSpan, FullSpan, NullSpan
from patchanalysis.signal.peaks import find_peak... |
9391093a3539f068a4e64393ad19fd4c79b71328392d36ebf91c66e49c939073 | Python | 3,255 | 87 | import shutil
from pathlib import Path
import pytest
from guppy.testing import compare_output_folders
from guppy.testing.api import locate_run_folder, step1, step2, step3, step4
from guppy_test_data import TESTING_DATA, event_ts_offset_for
SESSION_SUBDIRS = [
"SampleData_Clean/Photo_63_207-181030-103332",
"S... |
e2863c1a44b0bf1e2a8f514cd3d02e21ca4779689b67aa830c892f60eb7d21c5 | Python | 3,255 | 103 | """Creates markdown github wiki from bibtex files.
Use this version of pybtex for this code to work as expected: https://bitbucket.org/aurelienjaquier/pybtex/src/custom-style/
"""
import re
from pathlib import Path
from pybtex import PybtexEngine
from pybtex.style.formatting.unsrt import Style as OriginalStyle
from... |
9ad18f69ff72702b5aba4ba1374b8639e103dd49562025f809279284febd03dc | Python | 3,256 | 108 | import cv2
from pycocotools.coco import COCO
from pycocotools import mask as maskUtils
# coco id: https://tech.amikelive.com/node-718/what-object-categories-labels-are-in-coco-dataset/
all_instances_ids = [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 27, 28,
... |
83d9adbf004b7ebf8c7bb4ac187b68a2d8517bdf19589080202d1db9a63e1ea7 | Python | 3,259 | 110 | import numpy as np
import pytest
from tensorflow import keras
from dante.neural_surrogate import (
SurrogateModel,
AckleySurrogateModel,
RastriginSurrogateModel,
RosenbrockSurrogateModel,
GriewankSurrogateModel,
LevySurrogateModel,
SchwefelSurrogateModel,
MichalewiczSurrogateModel,
... |
34c89018cd4c23c23d5afc15a1f731b09a89293fd3571521d87125f12961c987 | Python | 3,260 | 96 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import os.path as osp
from typing import List
from mmengine.fileio import load
from mmseg.registry import DATASETS
from .basesegdataset import BaseSegDataset
@DATASETS.register_module()
class DecathlonDataset(BaseSegDataset):
"""Dataset for Dacathlon d... |
3a7e9ab1bf0da0ee7558e8a7833a4c27d03c76c324609d81195af622ab60fdb4 | Python | 3,260 | 112 | """basic scatter_sum operations from torch_scatter from
https://github.com/mir-group/pytorch_runstats/blob/main/torch_runstats/scatter_sum.py
Using code from https://github.com/rusty1s/pytorch_scatter, but cut down to avoid a dependency.
PyTorch plans to move these features into the main repo, but until then,
to make i... |
5a459778098106fbd8b7b6a8113f88fa340878597e529bf02f71bc383986e016 | Python | 3,261 | 88 | """Unit tests for the ``babel-clique-diff`` CLI (src/tools/clique_diff/cli.py).
Only the CLI layer — argument handling and the files it writes. The diff itself lives in
``src/model/compendium_diff.py`` and is tested in ``tests/model/test_compendium_diff.py``.
"""
import csv
import json
import pytest
from src.tools.... |
8c9e80c102726ef87feb29d74860e7369fd37ff4d0af8b06ee6ae76c4d0414bc | Python | 3,261 | 126 | from pathlib import Path
from functools import partial
import torch
import torch.nn.functional as F
from torch import sin, cos, atan2, acos
from einops import rearrange, pack, unpack
from equiformer_pytorch.utils import (
exists,
default,
cast_torch_tensor,
to_order,
identity,
l2norm
)
DATA_... |
547cc22f8eb283bd8fc8f4e50f9809b88b302e3432afa52e60914a9125a22260 | Python | 3,262 | 108 | from rest_framework.permissions import BasePermission
from .models import Benchmark
from benchmarkdataset.models import BenchmarkDataset
from benchmarkmodel.models import BenchmarkModel
from django.db.models import OuterRef, Subquery
class IsAdmin(BasePermission):
def has_permission(self, request, view):
... |
5e7686c77070f66c08c04512180ad0b61ad1e1c4edcdae8af340c3c463c47d2b | Python | 3,262 | 63 | """Related to issue https://github.com/spatialtopology/spacetop-prep/issues/110
We will remove events.tsv rows that are longer than the collected BOLD TR slices.
These cases will occur, when a scan was aborted earlier than expected,
but when the stimulus PC continued to collect data while scan operator was troublesho... |
bf27717f00419815c4473208e4caec8ab21e492cc67bd23c04b0535b2b943844 | Python | 3,262 | 102 | """Functions to create neuroml cell"""
"""
Copyright (c) 2016-2022, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as publishe... |
82a1e5628e22b46ffc26daaa9812640442b99b4067e53c6eb04e090df4a018b1 | Python | 3,263 | 127 | """Bookmarks REST API endpoints for room frame bookmarks."""
from fastapi import APIRouter
from sqlmodel import select
from zndraw.broadcast import broadcast_to_room
from zndraw.dependencies import (
AccessReadDep,
SessionDep,
SioDep,
WritableRoomDep,
)
from zndraw.exceptions import (
BookmarkNotF... |
b232ac73e2a5d74697df6d7794bfdd2915febdefd46875325abf420f56532908 | Python | 3,265 | 130 | """Dummy cell model used for testing"""
import bluepyopt.ephys as ephys
class DummyCellModel1(ephys.models.Model):
"""Dummy cell model 1"""
def __init__(self, name=None):
"""Constructor"""
super(DummyCellModel1, self).__init__(name)
self.persistent = []
self.icell = None
... |
98bee3029ca0ee9018403e236c35f092f04ff30ed757b773228737e13b87f347 | Python | 3,267 | 122 | import pytest
from kgx.prefix_manager import PrefixManager
@pytest.mark.parametrize(
"query",
[
("https://example.org/123", True),
("http://example.org/ABC", True),
("http://purl.obolibrary.org/obo/GO_0008150", True),
("GO:0008150", False),
],
)
def test_is_iri(query):
... |
a0cd6e71fce811c7dc7ac82aa8fcb975cb0aec12722ed67904c664363b8fd187 | Python | 3,267 | 93 | #!/usr/bin/env python
#
# Download data using http.
#
# Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import os
import sys
from typing import Sequence
import textwrap
from spinalcordtoolbox.download import install_named_dataset, DATASET_DICT, list_datasets, install_d... |
1166484c7dbd16485f7024af9a64b094bcaa20606061b6622a605f8bbeabbb4c | Python | 3,268 | 112 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
b67de74437550e4e8218d4df7df646cd9f19ade6bb3b770d038d501862d1f927 | Python | 3,268 | 86 | # SPDX-License-Identifier: Apache-2.0
"""Prepare the ImageNet dataset"""
import os
import argparse
import tarfile
import pickle
import gzip
from tqdm import tqdm
from mxnet.gluon.utils import check_sha1
_TARGET_DIR = os.path.expanduser('~/.onnx/datasets/imagenet')
_TRAIN_TAR = 'ILSVRC2012_img_train.tar'
_TRAIN_TAR_SH... |
ef079b433d283645ac01b9eb12636eac1ae082ea442d878ab5c5dc7d59569953 | Python | 3,268 | 73 | # For benchmark preprocessing usage:
#
# python Preprocessing_scFile.py --inputfile /home/wangjue/biodata/scData/allBench/9.Chung/T2000_UsingOriginalMatrix/T2000_expression.txt --outputfile /home/wangjue/biodata/scData/9.Chung.csv --cellcount 317 --genecount 2000 --split space --cellheadflag False
# python Preprocessin... |
b41d6ba36371be652f6d54b63788318a0e413362f025a13c74b68c695c64f663 | Python | 3,274 | 97 | import os
from pathlib import Path
from typing import Optional
import dotenv
import pytorch_lightning as pl
from omegaconf import DictConfig, OmegaConf
def get_env(env_name: str, default: Optional[str] = None) -> str:
"""
Safely read an environment variable.
Raises errors if it is not defined... |
6a46db2a7ddae0948d26b0ff2458f5ed4762c27ba06030ca48a0d5996fd888f7 | Python | 3,275 | 85 | import os
import re
import argparse
import pandas as pd
from concurrent.futures import ThreadPoolExecutor, as_completed
def parse_args():
parser = argparse.ArgumentParser(description="Check poisoning success from experiment results.")
parser.add_argument("--main_folder", type=str, required=True)
parser.add... |
8b899eff7a3af9fc67bb9f4fe8d907b22329187f997d717911828f6db0bacef6 | Python | 3,275 | 88 | """Context-Aware Implicit Neural Representations to Compress Earth Systems Model Data
DEVELOPED AT:
Department of Chemical Engineering
University of Utah, Salt Lake City,
Utah 84112, USA
DIRECTOR: Prof. Salah A Faroughi
DEVELOPED BY:
... |
277cad49f696df38723f4e706cc9b3d36e83c6f4c12820e51d97e408a96232d9 | Python | 3,276 | 82 | """
Comparing Picard and FastICA for the task of detecting ECG artifacts in MEG
===========================================================================
Picard and FastICA are fitted to MEG data, from several initializations.
The scores related to the detection of ECG artifacts are displayed for each
run. Picard i... |
baed4fb6da7b8f228f50f8f24906d84da96a45edff6d9205a8fc08dd71e18556 | Python | 3,276 | 120 | """
Helper script to combine coverage (as codecov seems to have problems...).
Written in python to be cross-platform
"""
import argparse
import os
from os import chdir, environ
from pathlib import Path
import platform
from pprint import pprint
import signal
from subprocess import PIPE, Popen, CalledProcessError, Timeo... |
61d17d4d952732463e192e30b983cf2f2ab85ed996f103596b735db51b3327af | Python | 3,277 | 96 | import os
import json
from utils import get_all_secrets, safe_store
def validate(secrets: dict):
"""main settings are expected to be a json file that contains secrets IDs of other objects"""
expected_keys = set(
[
"ca_config",
"intermediate_ca_key",
"intermediate_ca... |
0a2d9208fa82b7dd7f03a47ff3e4729f8ae44d5ee66640ee356b682285e81743 | Python | 3,278 | 96 | import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow.keras.layers import Conv2D, MaxPooling2D, \
UpSampling2D, Cropping2D, concatenate, ZeroPadding2D, SpatialDropout2D
import functools
def create(input_shape, num_class=1, activation=tf.nn.relu):
opts = locals().copy()
# model = De... |
6ff10946499cd0618925dfb5e94e081e44d1075cd9efaa51da1671f76af4768c | Python | 3,278 | 84 | import torch
import torch.nn as nn
import torch.nn.functional as F
from rde.modules.common.geometry import angstrom_to_nm, pairwise_dihedrals
from rde.modules.common.layers import AngularEncoding
from rde.utils.protein.constants import BBHeavyAtom
class ResiduePairEncoder(nn.Module):
def __init__(self, feat_dim... |
91bb879f17d6e9e7278015a146b01e5f6a444d801a8f8334d1881464f853ad8c | Python | 3,280 | 85 | # -*- coding:utf-8 -*-
'''
Author: MrZQAQ
Date: 2022-03-29 14:00
LastEditTime: 2022-11-23 15:32
LastEditors: MrZQAQ
Description: Test model
FilePath: /MCANet/utils/TestModel.py
'''
import torch
import numpy as np
import torch.nn.functional as F
from tqdm import tqdm
from prefetch_generator import BackgroundGenerator
f... |
f733bba2856cfa9c119515293262094f78757055aefa7e6cd841a26dc71539f3 | Python | 3,280 | 99 | from parse_cp_features import parse_cp_features
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
def visualize_channels(significant_features):
"""
Visualize the distribution of channels for significant features.
Parameters:
- significant_features: list, features found to be s... |
56b293b27b7735bb4f651c911823e51fed6772ff98c3a7a7acf07dbd45aa583b | Python | 3,281 | 66 | import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
from dgl.nn import GATConv
class GATEncoder(nn.Module):
"""Use multi-layer GATConv to extract graph structure node features"""
def __init__(self, in_features: int, out_features: int, num_heads: int = 1, activation=F.relu, k: ... |
ab872794af4f59514bc400cb3cfa09cc5a9cfaf7de4da844f450ea05a7ec6500 | Python | 3,281 | 86 | """Context-Aware Implicit Neural Representations to Compress Earth Systems Model Data
DEVELOPED AT:
Department of Chemical Engineering
University of Utah, Salt Lake City,
Utah 84112, USA
DIRECTOR: Prof. Salah A Faroughi
DEVELOPED BY:
... |
074395ba1b2e0a606a0fa6669d3e4de29c848b1583fa9fa95b022ac2a4b1bee3 | Python | 3,283 | 83 | import pandas as pd
from pathlib import Path
import subprocess
import os, sys
def extract_bids(filename: str, key: str) -> str:
"""
Extracts BIDS information based on input "key" prefix.
If filename includes an extension, code will remove it.
"""
bids_info = [match for match in filename.split('_') ... |
51fcada4b044e88a79017b0576d907a3f983938638043e141e7d337bfb18514c | Python | 3,283 | 65 | # -*- coding: utf-8 -*-
# Generated by Django 1.10.7 on 2017-07-26 20:49
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
import django.utils.timezone
class Migration(migrations.Migration):
"""Add a statistics summary table. This table stores aggregated d... |
94a89def718c01e6207822ffc3040d57ba6debad07ed8b033c03400df906873c | Python | 3,283 | 93 | import tensorflow as tf
# tf.enable_eager_execution()
from tensorflow.keras.layers import Conv2D, MaxPooling2D, \
UpSampling2D, Cropping2D, concatenate, ZeroPadding2D, SpatialDropout2D
import functools
from evidential_deep_learning.layers import Conv2DNormalGamma
def create(input_shape, activation=tf.nn.relu, num_... |
a88722316f1798fc4b265adc719d5542e5c5a0cc7f38f032362094463fb88e39 | Python | 3,284 | 90 | import ants
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
import scipy
import imageio
from skimage.color import rgb2gray
from scipy.ndimage import affine_transform
import cv2
from glob import glob
def calculate_affine(srcPoints, dstPoints):
# Add a fourth coordinate of 1 to each point
... |
cec53a72643fde2c51e46a6472d907a6caee0320e37ce1e1862b3218e021bb56 | Python | 3,284 | 132 | """Tests for multi-client synchronization via the ZnDraw Python client.
Two clients connected to the same room should see each other's changes
via REST API (no Socket.IO event propagation tested here — just data consistency).
"""
import ase
import numpy as np
from zndraw import ZnDraw
def _make_atoms(x: float) -> ... |
bc5773e519011bc4476413665d983eecdbe31eee657b6fed1201a3ceb7865909 | Python | 3,285 | 94 | ###########################################################################################
# Elementary tools for handling irreducible representations
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
#################################################################... |
cc17bb80e54264fb1383fe75334c188d3c0950939027b5209a5c74d989281efb | Python | 3,285 | 108 | import os
import subprocess
import tempfile
import numpy as np
import pytest
import xgboost as xgb
from xgboost import testing as tm
pytestmark = tm.timeout(10)
class TestOMP:
def test_omp(self):
dtrain, dtest = tm.load_agaricus(__file__)
param = {'booster': 'gbtree',
'objecti... |
cc57ac65c5fce6e4357ef98e70d8cff295ec2043e96c67d7c2f44ed8bc001d5d | Python | 3,285 | 78 | """Test functions in heudiconv.convert module.
"""
import pytest
from heudiconv.convert import (update_complex_name,
update_multiecho_name,
update_uncombined_name)
from heudiconv.bids import BIDSError
def test_update_complex_name():
"""Unit testing fo... |
565a76c4486f73297d0a4b32527f928c15b8b41508c7dd614f6f6fdacb77e31d | Python | 3,287 | 81 | # 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
#
# http://w... |
99d8ac167b550078ab54d37cb9dab8c4ce32cd1db70cb318d6e5d99dd0769753 | Python | 3,289 | 100 | # -*- coding: utf-8 -*-
# tests/test_moldata.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is free so... |
cf12c60e66914b84355f560d00e5ec1cec884ce5096c18cfa4f3437b3313cd73 | Python | 3,289 | 101 | """Test l5pc example"""
import os
import sys
import difflib
STOCHKV_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__),
'../../examples/stochkv'))
sys.path.insert(0, STOCHKV_PATH)
from bluepyopt import ephys
neuron_sim = ephys.simulators.NrnSimulator()
neuron... |
4ebcc290f67e659b3224e35f671a3d42cbe4cc15de6a33e52f2a808fde531242 | Python | 3,292 | 98 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
import torch
from chgnet.utils import (
cuda_devices_sorted_by_free_mem,
determine_device,
gpu_devices_sorted_by_free_mem,
solve_charge_by_mag,
)
if TYPE_CHECKING:
from pymatgen.core import Structure
def test_gpu... |
13bd7f660f1424f354cf5f9f95d39bc34ae9e2139ca0915abe9c6ed3502cf292 | Python | 3,294 | 115 | """
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 logging
from abc import ABC, abstractmethod
import torch
import wandb
from torch.utils.tensorboard import SummaryWriter
from ocpmodel... |
902eda80907af71269a896f18303bf51db3d64120b5ba852c511af242a611c66 | Python | 3,294 | 115 | """bluepyopt.ephys.simulators tests"""
"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as publis... |
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