sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6c66ff00b25df30aad047b4a566479209a5b45f8e6abda2505cb2ad919e2f525 | Python | 2,505 | 69 | from provdbconnector import ProvDb
from provdbconnector.db_adapters.in_memory import SimpleInMemoryAdapter
import pkg_resources
# create the api
prov_api = ProvDb(adapter=SimpleInMemoryAdapter, auth_info=None)
# create the prov document from examples
prov_document_buffer = pkg_resources.resource_stream("examples", "f... |
86e05289abe89905e6608fd3ba139f3e7d65ac8bac5181ee3e1889b0da4e71d8 | Python | 2,505 | 55 | # 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... |
7a8bdd92e2fdf2afda0b1c6959b6afd23a012e4b65e9274e0911d0dfecbf9d66 | Python | 2,506 | 58 | import numpy as np
import pandas as pd
def analyze_switch(
sub_data,
num_pre_switch_trials,
num_post_switch_trials,
switch_key="is_switch",
correct_key="is_correct_cue",
):
"""
Analyzes the choice accuracy window around rule switch events to create an average
learning curve (e.g., how ... |
826c336c862dc93191ea3f4473949cef4501c1968202081ee64a6e8c1d0f260c | Python | 2,506 | 64 | # %%
from urllib.request import urlretrieve
from bs4 import BeautifulSoup
import os
import shutil
# %%
def resolve_symlinks_in_html(url, save_path):
# Download the HTML file
urlretrieve(url, save_path)
# Parse the HTML file
with open(save_path, 'r') as html_file:
soup = BeautifulSoup(html_file... |
570491f5db27183ed59296373997159fb203dedea82c183001d36199e4cb377c | Python | 2,508 | 99 | from __future__ import annotations
from pathlib import Path
import sys
from nipype.utils.filemanip import which
import pytest
from heudiconv.cli.run import main as runner
from heudiconv.queue import clean_args
from .utils import TESTS_DATA_PATH
@pytest.mark.skipif(bool(which("sbatch")), reason="skip a real slurm ... |
b189760d5b15ddc9a1bea43f1585338acd25375ed119d1a50cd48769f87c7529 | Python | 2,509 | 70 | # SPDX-License-Identifier: Apache-2.0
import numpy as np
import cv2 as cv
from PIL import Image
import cityscapes_labels
def get_palette():
# get train id to color mappings from file
trainId2colors = {label.trainId: label.color for label in cityscapes_labels.labels}
# prepare and return palette
palett... |
f88184c9c088b894e2e56a15fe27ca0f4387b1d954ab873abe588666267aa43f | Python | 2,509 | 79 | from .common import *
@pytest.fixture(scope="session")
def adata_factory():
def adata_factory_(pca=False, n_top_genes=None, neighbors=False):
adata = sc.datasets.paul15()
adata.obs['celltype'] = adata.obs['paul15_clusters']
np.random.seed(42)
adata.obs['batch'] = np.random.randint(... |
2a4792a8f917bec78b747db9d2340a7f02749c775821f8c46e4c1bc7621c01e8 | Python | 2,510 | 97 | # CURIE prefixes used in Babel
#
# The point here is to keep prefixes in one place so that we can easily deal with things like PUBCHEM->PUBCHEM.COMPOUND
# In principle, we should generate this off of the context file?
MESH = "MESH"
NCIT = "NCIT"
CL = "CL"
CLO = "CLO"
GO = "GO"
FMA = "FMA"
UBERON = "UBERON"
SNOMEDCT = ... |
0e424b8a7238c94863e8e4a6f7be72bfccfe083d13eaa2067689f0a5484593f6 | Python | 2,512 | 75 | import click
import subprocess
from pathlib import Path
import pandas as pd
import torch
from allertrans.model import load_models, predict_ensemble
from allertrans.utils import load_h5_embeddings, load_esm_embeddings
model_protT5, model_cat = load_models()
@click.group()
def run_cli():
"""AllerTrans C... |
54ebe6d5d65725365c5e493fe3bcbccac4cc14ab3b5705cc07b698e0ed174b6e | Python | 2,512 | 49 | ## Restormer: Efficient Transformer for High-Resolution Image Restoration
## Syed Waqas Zamir, Aditya Arora, Salman Khan, Munawar Hayat, Fahad Shahbaz Khan, and Ming-Hsuan Yang
## https://arxiv.org/abs/2111.09881
## Download training and testing data for Defocus Deblurring task
import os
# import gdown
import shutil
... |
81eda826299c51425251f0279ae37835accc3915c6e70d0f0ef7d504077f64ba | Python | 2,512 | 81 | _base_ = './maskformer_r50-d32_8xb2-160k_ade20k-512x512.py'
checkpoint_file = 'https://download.openmmlab.com/mmsegmentation/v0.5/pretrain/swin/swin_tiny_patch4_window7_224_20220317-1cdeb081.pth' # noqa
backbone_norm_cfg = dict(type='LN', requires_grad=True)
depths = [2, 2, 6, 2]
model = dict(
backbone=dict(
... |
be636faa9483718955c64eff7ca2354747908821f8a4dc537d983ef005ee6399 | Python | 2,512 | 79 | checkpoint_file = 'https://download.openmmlab.com/mmsegmentation/v0.5/pretrain/swin/swin_small_patch4_window7_224_20220317-7ba6d6dd.pth' # noqa
_base_ = './maskformer_r50-d32_8xb2-160k_ade20k-512x512.py'
backbone_norm_cfg = dict(type='LN', requires_grad=True)
depths = [2, 2, 18, 2]
model = dict(
backbone=dict(
... |
c74374b0aa676a7861deaf4300826d06a191e014571c974b5b78ebb47f492569 | Python | 2,512 | 75 | from CybORG.Shared import Observation
from CybORG.Simulator.Actions import Action
from CybORG.Simulator.Actions.ConcreteActions.DensityScout import DensityScout
from CybORG.Simulator.Actions.ConcreteActions.SigCheck import SigCheck
class Analyse(Action):
""" Checks for malware on a single host.
Targets a sin... |
9f6352d3314d509812d5011503e634adb6717d88204545c05493fe2cdfd9dad3 | Python | 2,513 | 77 | 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
CONSISTENCY_CASES = [
(
"SampleData_csv/sample_data_csv_1",
... |
a593dd37c04c1eead9c41125817a5fb77b46237d4aeb7cccbc373084b92e05b2 | Python | 2,514 | 71 | """Filesystem extension for loading files from registered providers."""
import typing as t
from pathlib import Path
from fsspec.implementations.dirfs import DirFileSystem
from fsspec.implementations.local import LocalFileSystem
from zndraw.extensions.abc import Category, Extension
from zndraw.io import open_frames
... |
4fdd020e5670b2dabc5b1dc4505765cbe9ef92d752cca29552d13e8b426add38 | Python | 2,515 | 107 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 25 13:55:49 2023
@author: george
"""
import numpy as np
import pandas as pd
import pyqtgraph as pg
import os
import skimage.io as skio
from skimage.filters import threshold_otsu
from skimage import data, color, measure
from skimage.transform import... |
f746622feb2e089a3c745f4eba937f541b83a7d27ad123541583bcea6fa0d34f | Python | 2,515 | 85 | from copy import deepcopy
from medperf.exceptions import InvalidArgumentError
from medperf.tests.mocks.benchmarkmodel import generate_benchmarkmodel
import pytest
from medperf.commands.association.priority import AssociationPriority
TEST_ASSOCIATIONS = [
generate_benchmarkmodel(priority=0, model=1),
generate_... |
fc0d781747ede9f2fd33ae1f452c2552e403e8ea6998b79c0fc00053f5217b0f | Python | 2,515 | 68 | import shutil
from batchgenerators.utilities.file_and_folder_operations import *
import SimpleITK as sitk
from nnunet_mednext.paths import nnUNet_raw_data
if __name__ == '__main__':
#data is available at http://medicalsegmentation.com/covid19/
download_dir = '/home/fabian/Downloads'
task_id = 69
task... |
5bc081797d0ae985070bd842b0264360983a3c6f7e0aa5db0e6b558b9e309a52 | Python | 2,516 | 59 | import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
# Load the first Jacobian determinant map
# mouse jacobian
# jacobian_img_1 = nib.load('b0_correction_analysis/data/phantom_jacobian/jacobian_determinant_b0.nii')
jacobian_img_1 = nib.load('b0_correction_analysis/data/mouse_data/mouse_ph... |
f7fdddd352c6323cc0bff439ce85149be577916ca68efd665a5a1fe953042fa4 | Python | 2,517 | 71 | import requests
from medperf.exceptions import CommunicationRetrievalError
from medperf import config
from medperf.utils import remove_path, log_response_error
from .source import BaseSource
import validators
import os
class DirectLinkSource(BaseSource):
prefix = "direct:"
@classmethod
def validate_resou... |
fdf599e273636c95510435cecb80b7e34b62278c7a3d47d5e95b436528f7e600 | Python | 2,518 | 83 | from .ProvenanceObject import ProvenanceObject
from .extractor_cartridge import ExtractorCartridge
from .extractor_extension import ExtractorExtension
class Extractor(ProvenanceObject):
"""
This class represents and conceptual extractor.
Attributes:
- tag (str): Extractor tag.
- cartridge... |
e449ccc7d78517b57cdfec665b7cb888f1cdbdf0250859c8c8cef45130265bf2 | Python | 2,519 | 91 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
# pyre-strict
# pyre-ignore-all-errors[2,3]
from typing import Any, Dict, Iterable, Iterator, Tuple
from tabulate import tabulate
class Registry(Iterable[Tuple[str, Any]]):
"""
The registry that provides name -> object mapping, to suppor... |
6c8120210ac2c6c100c368b83f853e0621715bdd2b7d74b77ccd6dc405016947 | Python | 2,523 | 71 | import torch
def init_edge_rot_mat(edge_distance_vec):
edge_vec_0 = edge_distance_vec
edge_vec_0_distance = torch.sqrt(torch.sum(edge_vec_0**2, dim=1))
# Make sure the atoms are far enough apart
#assert torch.min(edge_vec_0_distance) < 0.0001
if torch.min(edge_vec_0_distance) < 0.0001:
... |
dad0b2f06fca6568e1ac6b4ca48657bf75727f29faeacb2b3990505b67f5a25a | Python | 2,523 | 82 | _base_ = [
'../_base_/models/san_vit-b16.py', '../_base_/datasets/coco-stuff164k.py',
'../_base_/default_runtime.py', '../_base_/schedules/schedule_160k.py'
]
crop_size = (640, 640)
train_pipeline = [
dict(type='LoadImageFromFile'),
dict(type='LoadAnnotations'),
dict(
type='RandomChoiceResiz... |
0edffde506b26fe84e24aeba831cbe96f16742390724486e9aa49618bdd257fa | Python | 2,525 | 77 | from fastapi import Query, Request, Form, APIRouter, status, Security
from fastapi.responses import HTMLResponse, RedirectResponse
from medperf.web_ui.auth import security_token, AUTH_COOKIE_NAME
from medperf.web_ui.common import templates, api_key_cookie, sanitize_redirect_url
from medperf.utils import print_web... |
33f4ca4cd7c11dbb077c119ba3ebfcadac936598a5c17b56f4afedc919e55a8f | Python | 2,525 | 72 | from __future__ import annotations
from typing import Any
import numpy as np
from CybORG.Agents.Wrappers import BlueEnterpriseWrapper
from ray.rllib.env.multi_agent_env import MultiAgentEnv
class EnterpriseMAE(BlueEnterpriseWrapper, MultiAgentEnv):
"""A wrapper designed to support CAGE Challenge 4 (RLlib Compat... |
56cb694dc7fca3141cf23c05d5c8cfc06520d5882e5d0180d96ff2397d3fbc9d | Python | 2,526 | 68 | import torch
from torch.optim import AdamW, SGD
from torch.utils.tensorboard import SummaryWriter
from torch.optim.lr_scheduler import CosineAnnealingLR, OneCycleLR
from yolov9_model import YOLOv9_GPU, YOLOv9_FPGA
from dataset_preprocessing import get_datasets, get_data_loaders
import torch.nn as nn
class FocalLoss(nn... |
d1fe3d81f28d554c784702550a9eac2a1fddef9fdd422070ed1788bbd5878f2b | Python | 2,526 | 87 | from __future__ import annotations
from glob import glob
import os
import os.path as op
from pathlib import Path
import shutil
import stat
import pytest
from .utils import TESTS_DATA_PATH
from ..parser import get_extracted_dicoms
def _get_dicoms_archive(tmpdir: Path, fmt: str) -> list[str]:
tmp_file = tmpdir /... |
d3ac93e9e158d00783e7996ec9ba4d3580a5369c247f4f297bf674d3d4864b77 | Python | 2,526 | 95 | from itertools import chain
from typing import Generator, Any, Dict, Optional
from kgx.config import get_graph_store_class
from kgx.graph.base_graph import BaseGraph
from kgx.source.source import Source
from kgx.utils.kgx_utils import sanitize_import
class GraphSource(Source):
"""
GraphSource is responsible ... |
7f322c361b988d461b6c6cb49ffbff83cebb7bc56e27a41d81f79a9345de39c3 | Python | 2,528 | 72 | # -*- coding: utf-8 -*-
# Albert Cardona 2014-11-21
# This file is meant to be run from within ./manage.py shell in the environment, like:
# [1] load export_all_csv.py
# [2] project_id = 12
# [2] export(project_id, "all")
from django.db import connection
from django.db import transaction
import gzip
def writeOneSkel... |
1d0f5e5770e3e27c748229e1d5f069f12ffda0e7f08d0a9fed02baf6e4fe10c4 | Python | 2,529 | 65 | import sys
sys.path.append('/home/luxin1/stGRL')
from stGRL import stGRL
import os
import torch
import pandas as pd
import scanpy as sc
from sklearn import metrics
import tqdm
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
sample_list = ['151507', '151508', '151509', '151510',
... |
b51bd422b4219f4b70a605d8d319ad58d97289bb6080eeca6e1d2e9945fc0f94 | Python | 2,530 | 69 | # tests/test_router_job_list.py
"""Tests for job listing and details endpoints using shared fixtures."""
import pytest
from conftest import make_room_address
from zndraw_joblib.exceptions import ProblemDetail
from zndraw_joblib.schemas import JobResponse, JobSummary, PaginatedResponse
@pytest.fixture
def multi_job_... |
f04940f171a3b69c316280694f1a38d4425dfd113128cb90509df39b510f86c1 | Python | 2,530 | 71 | import pytest
from unittest.mock import patch, MagicMock
from requests.exceptions import HTTPError
from neuprint import Client
from neuprint.tests import NEUPRINT_SERVER, DATASET
def test_arrow_endpoint_version_check():
c = Client(NEUPRINT_SERVER, DATASET)
# Test with version higher than 1.7.3
with p... |
68bdc3b97da82e43b01fad45583bde0dc5ad564d8eccd3fc99ee86fe28d10670 | Python | 2,531 | 93 | import os
import sys
import subprocess
from heudiconv.cli.run import main as runner
from heudiconv.queue import clean_args, which
from .utils import TESTS_DATA_PATH
import pytest
@pytest.mark.skipif(bool(which("sbatch")), reason="skip a real slurm call")
@pytest.mark.parametrize(
'invocation', [
"--files ... |
c82cab3f063d87393baec2f16bd911e5a39b8b61217be8756a7fe57f14eab890 | Python | 2,531 | 77 | #!/usr/bin/env python
import os
import sys
import time
import yaml
import hashlib
import argparse
from six.moves import urllib
required_keys = ['caffemodel', 'caffemodel_url', 'sha1']
def reporthook(count, block_size, total_size):
"""
From http://blog.moleculea.com/2012/10/04/urlretrieve-progres-indicator/
... |
07aac51f8b8862a1b85b8cada4c2f97196a43fdf87b57eba8e38f5115f487043 | Python | 2,532 | 59 | import imageio
from create_dataset import *
from utils import *
from PDFN import PDFN
from options import *
from saver import resume, save_img_single
from tqdm import tqdm
#from thop import profile
def main():
# parse options
parser = TestOptions()
opts = parser.parse()
# define mod... |
e0c9b017c62c83692a0c205f365209a0400aa408e85d4bb376405f37dee90d65 | Python | 2,532 | 90 | """Path tracing renderer configuration as a scene object."""
import enum
from pydantic import BaseModel, ConfigDict, Field
class EnvironmentPreset(enum.StrEnum):
"""HDRI environment preset options for path tracing."""
none = "none"
apartment = "apartment"
city = "city"
dawn = "dawn"
forest ... |
b6b4972739174eabb4f3599ad6ec43e8d5083760ce9cc0118e823c08342da718 | Python | 2,533 | 80 | from pysisyphus.constants import AU2EV, BOHR2ANG
from mace.calculators import mace_off_finetuned, mace_off
import torch
def get_mace_calculator(device="cpu", ver='finetuned'):
# Disable CUDA if using CPU to prevent CUDA initialization errors
if device == "cpu":
# Temporarily disable CUDA to prevent ini... |
3f906bb9538805b12bb922d06ca7e9af6e94471cf1923b25cc94740146a9b776 | Python | 2,534 | 65 | from grid_cell.lole import LOLE, LOCF
from grid_cell.manifold_fitter import label_mesh
from sklearn.linear_model import MultiTaskLasso, LinearRegression, LogisticRegression
from grid_cell.grid_cell_processor import Speed_Processor
from global_setting import *
def compute_locf(label, feamap, x_bound, y_bound, speed_mi... |
a39d1f996e395c2d3f4ad91572cc6dc9fe958c3e928536a39652d347cde3501d | Python | 2,534 | 74 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
from fastapi import FastAPI
from pydantic import BaseModel
import os
import sys
# 导入功能模块目录
sys.path.append("../")
from qa_chain.QA_chain_self import QA_chain_self
# os.environ["HTTP_PROXY"] = "http://127.0.0.1:7890"
# os.environ["HTTPS_PROXY"] = "http://127.0.0.1:7890"
... |
85698c1be8dc0ead09457e77caeffa76966b326d15cf857ec0e386835323ab94 | Python | 2,535 | 49 | # 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... |
be114c33749dfa1de946cb1ce14ae2804055d4bc47bbd659a53bd4fba84a18cc | Python | 2,535 | 77 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
from mmengine.config import Config, DictAction
from mmengine.utils import ProgressBar
from mmseg.registry import DATASETS, VISUALIZERS
from mmseg.utils import register_all_modules
def parse_args():
parser = argparse.ArgumentPa... |
c36ae02aab5838b721bbe9d7529f45e4bcd2baff025300edcc96f83e15e89faa | Python | 2,535 | 59 | import imageio
from create_dataset import *
from utils import *
from PDFN import PDFN
from options import *
from saver import resume, save_img_single
from tqdm import tqdm
#from thop import profile
def main():
# parse options
parser = TestOptions()
opts = parser.parse()
# define mod... |
b3837b54631bb6855e32bc7eee1109d9ae06c980a736deaf855066915e962ee0 | Python | 2,537 | 95 | """
Demo for using cross validation
===============================
"""
import os
import numpy as np
import xgboost as xgb
# load data in do training
CURRENT_DIR = os.path.dirname(__file__)
dtrain = xgb.DMatrix(
os.path.join(CURRENT_DIR, "../data/agaricus.txt.train?format=libsvm")
)
param = {"max_depth": 2, "et... |
8c637fc1f662d693d636b0d9314ccf636ca7c14db5b68f5769bfc9d5a73838d3 | Python | 2,538 | 72 | from behavior_analysis.experiment import PreyCaptureExperiment, TrialData
import numpy as np
import h5py
from sklearn.decomposition import PCA
from collections import defaultdict
if __name__ == "__main__":
# Experiment
directory = r"D:\percomorph_analysis"
video_directory = None
expt = PreyCaptureEx... |
ca8897d3cec42d8f3c1d6605297834585cbf5234ed701cb9fc664f7750728865 | Python | 2,538 | 85 | from collections import Counter
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
from simgen.analysis import (
BaseReport,
RDKitReport,
analyse_base,
analyse_rdkit,
)
from simgen.utils import initialize_mol
def test_analyse_base():
atoms = initialize_mol("C")
repo... |
e0ea47e729cfadad018544e13aab0ff1c35394043d12e5b0fc15261ffa8c81bf | Python | 2,538 | 67 | #!/usr/bin/env python3
# -*- coding:utf-8 -*-
###
# File: /root/CAMP/std_logger.py
# Project: /home/richard/projects/CAMP
# Created Date: Saturday, July 30th 2022, 3:51:24 pm
# Author: Ruochi Zhang
# Email: zrc720@gmail.com
# -----
# Last Modified: Sun Aug 28 2022
# Modified By: Ruochi Zhang
# -----
# Copyright (c) 202... |
3079a8664ab7a5d04e05143766401a582b4bfb3c4c8e747399ce7bb4d92f27c4 | Python | 2,539 | 57 | from grid_cell.util import compute_correlation_and_p_values
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import hickle as hkl
import os
from global_setting import *
def compute_corr(label, axes, fmt='.2f', feature_names=['x', 'y', 't', 'speed']):
correlation_matrix, p_value_matrix = com... |
68462d0c8bcf617ba5a29d3452550ff2f59ae9cf7e42ca06525dc2cb90758a29 | Python | 2,539 | 74 | '''Mixin class to make dictionaries'''
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
# Disabling lines below, generate error when loading ephys.examples
# from future import standard_library
# standard_library.instal... |
5ae5749d6ad59b3a03313f4555eb021339d7a3c69ef4a2e0ef03cbfc54ebeef6 | Python | 2,541 | 56 | import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
# Read the CSV files into DataFrames
df = pd.read_csv('../CSV/Predictions/auc_random_mol6710_classification.csv')
df2 = pd.read_csv('../CSV/Predictions/auc_random_mol6710_regression.csv')
df3 = pd.read_csv('../CSV/Predictions/auc_random_m... |
603a0263c4deb86570b017e3900a3af89418d6e172d117e4ff108c2c9cea26c9 | Python | 2,541 | 75 | import pytest
from unittest.mock import MagicMock, patch
import random
import numpy as np
import keras
from keras import ops
import matplotlib.pyplot as plt
import tsgm
def _get_labels(num_samples, output_dim):
labels = None
for i in range(num_samples):
sample = random.randint(0, output_dim - 1)
... |
9bd6286157a7be32d5b95c9521e06526f0696c51f9495ad0cfb5cb047c6d17d0 | Python | 2,542 | 75 | # %%
import os, glob
from os.path import join
# %%
def extract_bids_metadata(filename):
"""
Extract BIDS (Brain Imaging Data Structure) metadata from a given filename.
Parameters:
filename (str): The filename from which to extract metadata.
Returns:
dict: A dictionary containing the extracted ... |
ebb6b17c3c0f0927d939fbddf448bce452c2bcb56239604c90fa66def2b3796b | Python | 2,542 | 70 | import mne
from scipy.signal import detrend
import sys, os
from tqdm import tqdm
from glob import glob
import numpy as np
import itertools
import pandas as pd
import pickle
# go to base directory and import globals
base_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
#ptmp_dir = "/ptmp/kroma/m4d/"
os... |
ec51a538e3def7a8a10bf869b9c6e63cd6abdebd16539920dd14174caf16536c | Python | 2,543 | 61 | # -*- coding: utf-8 -*-
import json
from django.http import HttpRequest, JsonResponse
from django.shortcuts import get_object_or_404
from catmaid.models import UserRole, Project
from catmaid.control.authentication import requires_user_role
from catmaid.control.graph import _skeleton_graph
from catmaid.control.skelet... |
15ef1b5cfba0608d5d120c33c17ff350e1e6f15314324006f24eb0b1498d7f38 | Python | 2,546 | 87 | import logging
from fastapi import APIRouter, Depends, Form, Request
from fastapi.responses import HTMLResponse, JSONResponse, RedirectResponse
from medperf.entities.asset import Asset
from medperf.commands.asset.submit import SubmitAsset
from medperf.entities.model import Model
import medperf.config as config
from ... |
7063155cea306998f53cb844e31ed4b56b9a3011ab19e891a5490e491b0e66a6 | Python | 2,550 | 81 | import pytest
from medperf.exceptions import MedperfException
from medperf.commands.mlcube.utils import check_access_to_container
from medperf.tests.mocks.cube import TestCube
PATCH_UTILS = "medperf.commands.mlcube.utils.{}"
CONTAINER_ID = 1
USER_ID = 100
@pytest.fixture
def mock_user(mocker):
mocker.patch(
... |
6b3051204374920f9b2ed70a366b6e53635338aa4611dc3e0bfeae2f002bd201 | Python | 2,553 | 47 | """medperf URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/3.2/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: path('', views.home, name='home')
Class-based... |
47b1f872de3fb95323fd5932ca03b28d939e7201ef76e05b5a7a4190ce343aa0 | Python | 2,554 | 79 | import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from pathlib import Path
base_path = Path("aDBS_UPDRS.csv")
df = pd.read_csv(base_path)
metrics = ['total_updrs_iii_score', 'updrs_iii_bradykinesia', 'updrs_iii_tremor', 'updrs_iii_rigidity']
metric_labels = ['Total MDS-UPDRS III Score','Brady... |
75a0993843a06a3f43751aeb13f750998ba880753900ae0bfe8670937f7497d9 | Python | 2,554 | 67 | from os import path as osp
from torch.utils import data as data
from torchvision.transforms.functional import normalize
from basicsr.data.data_util import paths_from_lmdb
from basicsr.utils import FileClient, imfrombytes, img2tensor, scandir
class SingleImageDataset(data.Dataset):
"""Read only lq images in the t... |
77ab503b7780c11cb7c99d41e96b9c108de45b50dec95dd52e3f86f973534ea5 | Python | 2,554 | 83 | from nnunet_mednext.network_architecture.mednextv1.MedNextV1 import MedNeXt
def create_mednextv1_small(num_input_channels, num_classes, kernel_size=3, ds=False):
return MedNeXt(
in_channels = num_input_channels,
n_channels = 32,
n_classes = num_classes,
exp_r=2, ... |
14d58c0853b902feca69b80dc10acb0f5a841667530c53a90009e34a48c63efb | Python | 2,555 | 56 | #!/usr/bin/env python
"""
Use the openmoltools wrappers of OpenEye and Antechamber to rebuild input files
for the FreeSolv database.
Looks for freesolve database using environment variable FREESOLV_PATH
Outputs two LOCAL directories of files: ./tripos_mol2/ and ./mol2files_gaff/
"""
import os
import openmoltools
impor... |
87816616474ad9fa0aa53860f1aa594b39822ca0dd0e05649c8413602f500206 | Python | 2,555 | 86 | # written by Lee Hwee Kuan, 31Dec2021
# written by Lee Hwee Kuan, 11Feb2022
#
# the problem with cosine annealing is that the lr oscillates and
# at larger lr, it can throw off the optimiser. usually cosine lr
# scheduler is use for small enough max lr. added a functionality
# that have a decay max lr but operate li... |
cfcb9ccc774eb16ee7a99a3a8b62abb02f74e886be815b9464ba80770c214947 | Python | 2,555 | 98 | from medperf.exceptions import InvalidArgumentError
import pytest
from medperf.commands.benchmark.update_committee_members import UpdateCommitteeMembers
def test_both_file_and_list_raises():
# Act & Assert
with pytest.raises(InvalidArgumentError):
UpdateCommitteeMembers(
1,
co... |
70185abcf616fb36081fb63c7b12c91dea54fdf53cce3e992ce0273b61e7f502 | Python | 2,556 | 90 | import os
import shutil
from utils import get_collaborator_cn
def collaborator_pre_training_hook(
data_path,
labels_path,
node_cert_folder,
ca_cert_folder,
plan_path,
output_logs,
init_nnunet_directory,
workspace_folder,
):
import nnunet_setup
cn = get_collaborator_cn()
o... |
d89ffce1dbdd9ba06e7b4554bd2053becc91932f47b63754d653856cced9ae79 | Python | 2,559 | 75 | # MagellanMapper unit testing for detector
"""Unit testing for the MagellanMapper detector module."""
import unittest
import numpy as np
from magmap.cv import detector
class TestDetector(unittest.TestCase):
def make_random_blobs(self) -> "detector.Blobs":
"""Make blobs with random coordinates.
... |
18dd13ae327d11264a60f782629c2f3a5fdf7b1bd924467378e3fea3a72170e3 | Python | 2,561 | 79 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
from torch import nn as nn
from torch.nn import functional as F
class LinearAttention(nn.Module):
"""Multi-Head linear attention proposed in "Transformers are RNNs".
Source: https://github.com/KU-CVLAB/CAT-Seg/blob/main/cat_seg/modeling/transformer... |
824706009b2f87607d9d684fd730fd87fd66ee8341e075ee01a072f2be05c8ea | Python | 2,561 | 70 | """Unit testing for the chunking module"""
import unittest
from typing import Sequence
import numpy as np
from magmap.cv import chunking, detector
from magmap.settings import config
class TestChunking(unittest.TestCase):
@staticmethod
def stack_split_remerge(
roi: np.ndarray, max_pixels: S... |
76420afa7f91ae784cef0ef9c92292b00f6c0ee86dc57f8036f55e1756d27e80 | Python | 2,565 | 58 | import nibabel as nib
import numpy as np
from sklearn.preprocessing import normalize
from nilearn import masking
def filter_voxels_by_patient_count(lesion_files, min_patient_count, normalize_vector, output_folder):
"""
Filter voxels by the number of patients they are involved in.
"""
no_of_pat... |
c4d5e7c02d498f2b9f0ea3c5cb88bf3fedaa5b01a6a13fe8c7c285564b77d55c | Python | 2,565 | 65 | import io
import pickle
from pathlib import Path
from typing import Callable, Optional, Tuple, Sequence, Union
import numpy as np
import torch
class DiskCachedDataset(torch.utils.data.Dataset):
def __init__(self, dataset:Sequence,
cache_path: Union[str, Path],
num_copies: int = ... |
552924f21cb8737c4dd7bd222f084839cc282eac208517bee9f2d1e73c2b25bc | Python | 2,566 | 70 |
from CybORG.Agents import BaseAgent
from CybORG.Shared import Scenario
from CybORG.Shared.RewardCalculator import RewardCalculator
class ScenarioGenerator:
"""The ScenarioGenerator class is an abstract class that defines the interface for other ScenarioGenerator classes.
Attributes
----------
updat... |
642c6c588330f664f31d000877eb83fc4ac32ce7a600bca245d13e99cedc545f | Python | 2,567 | 89 | import os
import argparse
import SimpleITK as sitk
import numpy as np
def check_subject_validity(subject_dir):
"""Checks if a subject folder is valid.
Args:
subject_dir (str): The subject folder.
Returns:
bool: True if the subject folder is valid, False otherwise.
"""
subject_va... |
cad2b558644c233b69b254ef26f0389a41781f60443a6515356e35aecba17698 | Python | 2,568 | 59 | from jaxkineticmodel.load_sbml.sbml_model import SBMLModel
import jax.numpy as jnp
from jaxkineticmodel.utils import get_logger
from jaxkineticmodel.simulated_dbtl.dbtl import DesignBuildTestLearnCycle
logger = get_logger(__name__)
# load model (Messiha et. al (2013))
filepath = ("models/sbml_models/working_models/Mes... |
28ea1576377c781eb0aa406a155658aed857266f9c0956d749b6feec6d31edbf | Python | 2,569 | 67 | import medperf.config as config
from medperf.entities.aggregator import Aggregator
from medperf.entities.training_exp import TrainingExp
from medperf.entities.cube import Cube
from medperf.utils import remove_path
class SubmitTrainingExp:
@classmethod
def run(cls, training_exp_info: dict):
"""Submits ... |
57e32e17d65d4c2d0076f424e07642aad40e1c9e998e437af61ec3595e961b6a | Python | 2,571 | 67 | #!/usr/bin/env python3
# -*- coding:utf-8 -*-
###
# File: /root/CAMP/std_logger.py
# Project: /home/richard/projects/pepland/inference/cpkt/model/code/utils
# Created Date: Saturday, July 30th 2022, 3:51:24 pm
# Author: Ruochi Zhang
# Email: zrc720@gmail.com
# -----
# Last Modified: Sat Dec 23 2023
# Modified By: Ruoch... |
b7f3dcaf7abb080f6285d01f28a69c1ca817dcd8a5f2da1deaff488eee4b0097 | Python | 2,572 | 62 | """Live contract tests for :mod:`guppy.utils.dandi_filter`.
These hit the real DANDI Archive and are intended for **local use only**. They are deselected in
CI (see ``.github/workflows/run-tests.yml``) because the archive is subject to network flakiness
and its contents change as datasets are published.
Run locally w... |
5cac0f2022d8bc319e8e332d13c85feedc8c80961ba0661666a9889055ee3173 | Python | 2,574 | 70 | # pytest unit tests for sct_crop_image
import pytest
import logging
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.scripts import sct_crop_image
from spinalcordtoolbox.utils.sys import sct_test_path
logger = logging.getLogger(__name__)
@pytest.mark.sct_testing
@pytest.mark.parametrize("path_in,pa... |
d7ef027834322b4ea0e10a7344723647b7a78993c523a33d73ea337397070ddd | Python | 2,574 | 53 | import catmaid.fields
import datetime
from django.conf import settings
import django.contrib.postgres.fields.jsonb
import django.contrib.postgres.functions
from django.db import migrations, models
import django.db.models.deletion
forward = """
ALTER TABLE catmaid_deep_link DROP CONSTRAINT catmaid_deep_link_active... |
5483b4f1490280ea2e44f3cdea23256f6c2fb667a4badde3f54d3b7a2ade5791 | Python | 2,575 | 66 | import yaml
import typer
from prepare import prepare_data
from sanity_check import check
from stats import get_stats
app = typer.Typer()
@app.command("prepare")
def prepare(
data_path: str = typer.Option(..., "--data_path"),
labels_path: str = typer.Option(..., "--labels_path"),
params_file: str = typer.... |
757e69a1af34ea38aeac69bdbe93030d273dd1a93662f3ed10ae63e8b9a217df | Python | 2,575 | 96 | """Smoke tests confirming APSO works as used in the Poison26 singularity container.
Mirrors the workflow in manuscripts/Poison26/bin/attack/poison_MNIST.py.
"""
import pytest
import torch
import torch.nn as nn
from Adversarial_Observation.Swarm import PSO
IMG_DIM = 1 * 28 * 28
N_PARTICLES = 10
TARGET_CLASS = 3
@pyte... |
870900d68c15f4a4a2cd21d72a57d886b496d0ed65cf0ebf5de6868f19323073 | Python | 2,576 | 84 | import os
from grid_cell.gkr_fitting_helper import load_and_process_data, fit_gkr_models
import hickle as hkl
import numpy as np
from global_setting import *
dataset_name = ['r1m1', 'r1m2', 'r1m3', 'r2m1', 'r2m2', 'r2m3', 's1m1', 'q1m1', 'q1m2']
preprocessed_file_name = 'preprocessed_data_OF.hkl'
n_sample_data = 10000... |
2a98693b532536b9e1dfdfa6abf870a2b74be93f0fda45b9b98134f05871debc | Python | 2,577 | 76 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmseg.models.decode_heads import ASPPHead, DepthwiseSeparableASPPHead
from .utils import _conv_has_norm, to_cuda
def test_aspp_head():
with pytest.raises(AssertionError):
# pool_scales must be list|tuple
ASPPHead(in_... |
a1411fd7135235f982e0c9ace3c717baaa56500d2c31aa947d705a13d7566d02 | Python | 2,579 | 59 | import os
from concurrent.futures import ThreadPoolExecutor, as_completed
# Path to your main folder
#main_folder = '/work/hdd/bbse/wklai/AdversarialData/APSO_Poison/manuscripts/POISON25/MNIST_train_model1'
main_folder = '/work/hdd/bbse/wklai/AdversarialData/APSO_Poison/manuscripts/POISON25/MNIST_train_model2'
def pr... |
beb5518f4a519ab9168e11784fa5aaf623d0ae82cafa3a9164a76f749210b81a | Python | 2,580 | 69 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import warnings
from mmengine import Config, DictAction
from mmseg.apis import init_model
def parse_args():
parser = argparse.ArgumentParser(description='Print the whole config')
parser.add_argument('config', help='config file path')
parser... |
f7a032b779acb0822d94238883c7272bb4fb94b43324b5cb4fac1ad91320ccd9 | Python | 2,580 | 63 | import numpy as np
import torch
from torch.utils.data import Dataset
class SyntheticVisualFlowDataset(Dataset):
def __init__(self, num_samples=1000, dimensions=8, max_value=1, var_scaler=0.01, speed_func="random", num_speeds=11):
assert speed_func in ["random", "random_walk", "mismatch"]
assert di... |
79d579faedca3f46c17cec7e91e4f55994319572576902bb5412bf702554d736 | Python | 2,581 | 76 | """
Script to create symbolic links to data sources (to enable easier handling
when training on different machines)
"""
import os.path
import glob
import numpy as np
from utils import *
# input and output folders:
folder_in_WS = ("/PATH1/TO/CONVERTED/RAW/DATA/")
folder_in_WS_sim = ("/PATH1/TO/SIMULATED/DATA/")
folder_... |
c771e95a76d398f90d5904ffd699b934f13feccd7fbeaf88ef62c243dc4138b9 | Python | 2,582 | 79 | import os
import random
import json
from tqdm import tqdm
import argparse
import pathlib
import openai
openai.organization = os.getenv('OPENAI_ORG')
openai.api_key = os.getenv('OPENAI_API_KEY')
from load_aokvqa import load_aokvqa
random.seed(0)
def main():
parser = argparse.ArgumentParser()
parser.add_arg... |
8b94cdafffb06dfdae98d71c5155b49ad11ed8460f3b5d079a82b85375ccb687 | Python | 2,583 | 82 | import seaborn as sns
import pandas as pd
from qtools.data_tracking import metadata
from qtools.variable_output_dims import (
create_lineplot,
calculate_quartet_scores,
calculate_losses,
calculate_non_zero_features,
load_json_as_table
)
# Configuration
MODEL_TYPES = ['siameseloss', 'quartetloss',... |
b9071ef4db4e4374c9aca2650b26c14e32983152ab5646f5b6eb4023b5ff69f2 | Python | 2,587 | 84 | import sys
import os
import time
import random
pwd = os.getcwd()
# Print all command line arguments
for i, arg in enumerate(sys.argv):
print(f"Argument {i}: {arg}",flush = True)
# Print all command line arguments
random_sleep_time = random.uniform(5,10)
print("Start : %s" % time.ctime(),flush = True)
time.sleep( ... |
ca59af61de932669c0b54cd4010a0d7dad8487b73883520d4e17a18f048b8b2d | Python | 2,587 | 68 | """
Example of training controller with NVFlare
===========================================
"""
import multiprocessing
from nvflare.apis.client import Client
from nvflare.apis.fl_context import FLContext
from nvflare.apis.impl.controller import Controller, Task
from nvflare.apis.shareable import Shareable
from nvflare... |
dbc1e72e5fa754cdc451382f914ebbe9cb2a593af9e9bd48b883b4c0601b453b | Python | 2,589 | 58 | from CybORG.Shared import Observation
from CybORG.Simulator.Actions.ConcreteActions.TargetedLocalAction import TargetedLocalAction
from CybORG.Simulator.Host import Host
from CybORG.Simulator.Process import Process
from CybORG.Simulator.State import State
class StopProcess(TargetedLocalAction):
""" A sub-action f... |
ec2ad336c699d1d24fe77deb248c4b5bc75d08e40062d7325b0760c0fdd963f3 | Python | 2,589 | 95 | """MLCube handler file"""
import typer
import subprocess
app = typer.Typer()
def exec_python(cmd: str) -> None:
splitted_cmd = cmd.split()
subprocess.run(splitted_cmd, cwd=".", check=True)
class PrepareTask(object):
"""
Task for preparing the data
Arguments:
- data_path: data locat... |
36dca75fd607a262a6498df9e9908749cf9dcf2490f8e76a497786675eebe22c | Python | 2,590 | 102 | import os
from kgx.transformer import Transformer
from tests import RESOURCE_DIR, TARGET_DIR
def test_jelly_roundtrip_basic():
"""
Test basic roundtrip: transform TSV to Jelly format and back.
"""
input_args = {
"filename": [
os.path.join(RESOURCE_DIR, "graph_nodes.tsv"),
... |
6b816d5d13fbe56ccba9f81f096d554013380c6430ee5be5c5408237714fc2b5 | Python | 2,590 | 88 | # model settings
backbone_norm_cfg = dict(type='LN', eps=1e-6, requires_grad=True)
norm_cfg = dict(type='SyncBN', requires_grad=True)
data_preprocessor = dict(
type='SegDataPreProcessor',
mean=[123.675, 116.28, 103.53],
std=[58.395, 57.12, 57.375],
bgr_to_rgb=True,
pad_val=0,
seg_pad_val=255)
mo... |
07ee84bed2383a89f59eae715c4afabf849d04bcef158da3d5022e70be4485f2 | Python | 2,591 | 102 | # -*- coding: utf-8 -*-
import argparse
import math
# Respected precision
epsilon = 0.001
def same(a, b, eps=epsilon) -> bool:
return abs(a - b) < eps
class Point3D:
"""A simple container to hold three coordinate values.
"""
def __init__(self, x, y, z):
self.x, self.y, self.z = x, y, z
... |
d417a6225ecb789e1aac4e3cc60ba7b8bafe05e65a743b47cd2f4e363c1dd2b1 | Python | 2,591 | 88 | # model settings
backbone_norm_cfg = dict(type='LN', eps=1e-6, requires_grad=True)
norm_cfg = dict(type='SyncBN', requires_grad=True)
data_preprocessor = dict(
type='SegDataPreProcessor',
mean=[123.675, 116.28, 103.53],
std=[58.395, 57.12, 57.375],
bgr_to_rgb=True,
pad_val=0,
seg_pad_val=255)
mo... |
16333c44f844127e9a0511275dbc8469b6bf2c034440f61034c847a5fdb3e9dd | Python | 2,593 | 80 | """Experimental support for MPI."""
import inspect
import os
import re
from collections.abc import Mapping, MutableMapping
from typing import TypeVar
from schema_salad.utils import yaml_no_ts
MpiConfigT = TypeVar("MpiConfigT", bound="MpiConfig")
MPIRequirementName = "http://commonwl.org/cwltool#MPIRequirement"
cl... |
e62b0359d1fa6b0c85d4187c2c1dc7306d2b6c4ebf405565990786985fc63684 | Python | 2,594 | 54 | # Provided by the FeTS Initiative (www.fets.ai) as part of the FeTS Challenge 2022
# Contributing Authors (alphabetical):
# Brandon Edwards (Intel)
# Patrick Foley (Intel)
# Sarthak Pati (Intel)
# Micah Sheller (Intel)
"""This package includes dependencies of the fets project."""
from setuptools import setup
with ... |
91ed0b7dd4ad05b12c4c46529d8cd90d20ed8b07ef70959345e6d305e671dd48 | Python | 2,597 | 70 | #!/usr/bin/env python3
# -*- coding:utf-8 -*-
###
# File: /home/richard/projects/biology_llm_platform/mlm/pepland/inference.py
# Project: /home/richard/projects/biology_llm_platform/mlm/pepland
# Created Date: Thursday, November 28th 2024, 10:05:57 am
# Author: Ruochi Zhang
# Email: zrc720@gmail.com
# -----
# Last Modi... |
9369fefa92aa6845f8f9734e84f4e3d5b544d155dfe96f85b08a5933b495fcab | Python | 2,597 | 84 | import logging
from typing import Optional
import torch
from torch import nn
from ocpmodels.common import distutils
class L2MAELoss(nn.Module):
def __init__(self, reduction: str = "mean") -> None:
super().__init__()
self.reduction = reduction
assert reduction in ["mean", "sum"]
def ... |
d7bb787e7576274097fdb02d34583fa13f0f626646bbaef07b6abc8e016500fb | Python | 2,597 | 83 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 13 17:33:14 2023
@author: george
"""
import warnings
warnings.simplefilter(action='ignore', category=Warning)
import numpy as np
import pandas as pd
from distutils.version import StrictVersion
from tqdm import tqdm
import os, glob, sys
import skim... |
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