sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c86537f11d41fd27df40a021881ef7f3e5f57a85b7a581a76363a2202a755049 | Python | 1,612 | 49 | # @license
# Copyright 2025 Google Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... |
f6fe5f40d43d673d8b96546fde8348dfa82985b568e9d736001d5f1142d2e858 | Python | 1,613 | 51 | import sys
from unittest import mock
import pytest
from ci.ray_ci.bisect.bisector import Bisector
from ci.ray_ci.bisect.macos_validator import MacOSValidator
from ci.ray_ci.bisect.validator import Validator
from ray_release.test import Test
class MockValidator(Validator):
def __init__(self, return_value: bool)... |
20930878f0ac52ff508f68237add1c45c623e8fafa780f6a92d08b5811c8f3f7 | Python | 1,614 | 52 | # Generated by Django 4.1.5 on 2023-05-29 17:54
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
("infer", "0017_auto_20230526_0316"),
]
operations = [
migrations.CreateModel(
name="ProteomeTask"... |
bab55a30a8f6bf2fd17dddc1780a6d61408cb76744885e377fdaba84fdafccee | Python | 1,615 | 45 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import torch
import torch.nn.functional as F
class Act(torch.nn.Module):
def __init__(self, act: ... |
3aa027b96d927f0f72fdb0fc7bb16eea3587fad9b0dcf94ca5f1551e87135c56 | Python | 1,616 | 62 | """
Quickstart: vLLM + Ray Data batch inference.
1. Installation
2. Dataset creation
3. Processor configuration
4. Running inference
5. Getting results
"""
# __minimal_vllm_quickstart_start__
import ray
from ray.data.llm import vLLMEngineProcessorConfig, build_processor
# Initialize Ray
ray.init()
# simple dataset
... |
858bb82af4b1bc98807e6e5f0c8f201415645eeb1150de7a0048afa68e75a8d5 | Python | 1,616 | 34 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
2fdfcc206bf2b686e1680d3556d72a2e8631233fdc1bf990278ae4fc4f465870 | Python | 1,617 | 63 | # -*- coding: utf-8 -*-
"""
"""
import numpy as np
import pytest
import vtkplotlib as vpl
pytestmark = pytest.mark.order(6)
def test_plot():
t = np.arange(0, 1, .001) * 2 * np.pi
vertices = np.array(
[np.cos(2 * t),
np.sin(3 * t),
np.cos(5 * t) * np.sin(7 * t)]).T... |
a5ee2bd4164243af41d73b8e3e76b4ab5664be1e776cd572f126133e842c9f2a | Python | 1,618 | 47 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------
# Created By : Kangjoo Lee (kangjoo.lee@yale.edu)
# Last Updated: 08/06/2024
# -------------------------------------------------------------------------
# Imports
import matplotlib.pyplot as plt
... |
1b9c073cd71a48da606be50f7e9eb32adcab3f6a2bb0661672ce70b83a517893 | Python | 1,619 | 42 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
85be7536a197c8a1e99e7f46a7bdb4ab8aaf38aa6792b1c08a4b7613385668cc | Python | 1,620 | 53 | from typing import Sequence, Any
from numbers import Number
from functools import partial
import numpy as np
import jax
import jax.numpy as jnp
from jax.lax import with_sharding_constraint
from jax.sharding import SingleDeviceSharding, PositionalSharding
def is_sharded_array(array: Any) -> bool:
if isinstance(arr... |
da9a6762dec993db8003a43c54a32a91e267e6f6ee618b6c64f20f11fe02fcb7 | Python | 1,620 | 35 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
4ea01dc13bca23d169a57ee4e3c207cd961ca9ecf09478dd0c3b115212509a27 | Python | 1,621 | 51 | #!/usr/bin/env python
"""
Useful utilities for working with pysam variant objects
"""
def get_info_field(record, name, singularize=False):
if name not in record.info:
if name == 'SVLEN':
if record.info['SVTYPE'] in ['DEL', 'DUP', 'INV']:
record.info['SVLEN'] = record.stop - re... |
f3b7f197d17370bda11d98c2564dcde4c494102a3d866193c359c3bfbc049d13 | Python | 1,621 | 48 | # built-in dependencies
from typing import Any, List, Union
# project dependencies
from deepface.commons.onnx_utils import build_session
from deepface.models.facial_recognition.onnx.OnnxFacialRecognition import OnnxFacialRecognition
from deepface.commons.logger import Logger
logger = Logger()
# pylint: disable=line-... |
af2665e855ec5682277c4166c1a701303ad321a7f426bcb30775ed553b043b83 | Python | 1,622 | 64 | # Calculate the whole brain injury degree for a single impact case
# and write it into 'injury_degree'
# Steps:
# 1. Extract response peaks from the raw data.
# 2. Manually set injury thresholds.
# 3. Calculate element injury degrees at different thresholds according
# to the definition of injury degree. The whole bra... |
b0bb0809878b302cd68b4620c3c64f7e5dbaf09ab12cd2009286058573823f32 | Python | 1,622 | 48 | #!/usr/bin/env python
#Lexi Morrissey, Mahony Lab @ Pennsylvania State University
#Contains method for predicting whether area should receive multimapped reads via pre-trained CNN in Allo.
import os
import absl.logging
absl.logging.set_verbosity(absl.logging.ERROR)
import contextlib, io
import logging
os.environ['TF_C... |
bb98c0e136fe4a9e8fa3a38c39837af06b8a9695bbbff96bc42433e6f3f15bdd | Python | 1,622 | 46 | import numpy as np
import pandas as pd
import sklearn.metrics
def decide_stertor_pred(row, threshs):
"""Pick class from logits using NNRank method"""
row_classif = row > threshs
for i in range(4):
if not row_classif[i]:
return int(max(i - 1, 0))
return 3
full_df = pd.read_csv("an... |
ad923d398392cd0b03c7d54851a7456feb5f72d669ca2045e105901204f9ae47 | Python | 1,623 | 43 | import numpy as np
import torch
from ..utils import common_functions as c_f
from ..miners.base_miner import BaseSubsetBatchMiner
class MaximumLossMiner(BaseSubsetBatchMiner):
def __init__(self, loss, miner=None, num_trials=5, **kwargs):
super().__init__(**kwargs)
self.loss = loss
self.min... |
2a7f58ca14719e269b2e4471f78a9cfd6953cb564ddc4f92fe8eb05385440dea | Python | 1,624 | 51 | import glob
import geopandas as gpd
import numpy as np
import os
import pandas as pd
import rasterio as rio
from src import patches
from src import neon_paths
from src.data import read_config
from src.start_cluster import start
from distributed import wait
config = read_config("config.yml")
shapefiles = glob.glob("/or... |
454d02be808a46bb8061a37e64367b7f3f5efddb42289e7d55d774cfa5651be7 | Python | 1,624 | 46 | #this script with assistance from ChatGPT3.5 20231204
# the function is to create a mean of all the normalized images
# python nii2meanLesion.py
import os
import nibabel as nib
import numpy as np
import fnmatch
def create_mean_image(folder_path, output_path):
# Ensure the output folder exists
os.makedirs(os.... |
4e08d9eecb3cb3d11a61afc39de7d01fc601bda53c8b8c858354c36cb19fb052 | Python | 1,624 | 49 | from __future__ import annotations
from typing import Any
import attrs
from snakebids import bidsapp
from snakebids.plugins.base import PluginBase
# last rules in each chain that populates the cache dir (HIPPUNFOLD_CACHE_DIR);
# their upstream download rules (download_surf_template_atlas,
# download_nnunet_model) ar... |
5b2ec4419d22eab30ec6e2d4a1b5252b0611d92c003fd431179874c9ba8dfaeb | Python | 1,624 | 49 | import numpy as np
import scipy.sparse as sparse
from hic3defdr.util.clusters import find_clusters
def classify(row, col, value, clusters):
"""
Classifies pixels (specified by row, col coordinates) into classes
(corresponding to the columns of value) where their value is highest,
ignoring those pixel... |
e54a7d702d62c476095eebd3a0d3fe96b7d194efc0f54c77ff1e5136e12bb682 | Python | 1,624 | 53 | import numpy as np
import math
from .basic_distributions import Distribution
from ..utils import *
class Poisson(Distribution):
"""
Class to define Poisson distributions.
Equations:
p(x|theta) = theta**x * exp(-theta) * 1/theta!
log p(x|a,b) = x*theta - theta - log(x!)
E[x] = theta
var[x... |
832280c3d47213ab31569f34967115299a1dcdc38fcfd1da851a76b3a94b57db | Python | 1,625 | 39 | import numpy as np
from rich import print
from siapy.datasets.tabular import TabularDataset
from siapy.entities import Shape, SpectralImage, SpectralImageSet
# Create two mock spectral images with dimensions 100x100 pixels and 10 bands
rng = np.random.default_rng(seed=42)
image1 = SpectralImage.from_numpy(rng.random(... |
fb852c154806903b40824e7c64e4e5f2e23ac1e7c1866a8c43d7de6ad5b1a777 | Python | 1,626 | 49 | """Create two augmented views per ECG for contrastive self-supervised learning."""
import torch
from torch.utils.data import DataLoader, Dataset
import ecg_augmentations as ea
FS = 500
augment = ea.Compose(
[
ea.RandomCrop(duration=8, fs=FS),
ea.RandomApply([ea.BaselineWander(FS), ea.GaussianNoi... |
ace423bc092a94e2411d90ffaa04336c1d15e1f8ac5dfc0b3d328ca4468a55a4 | Python | 1,628 | 38 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
ed47b9e67055984baa976e184169a588285fa75b22fa96c0513de10f89577357 | Python | 1,628 | 53 | """Functions related to randomized SVD."""
# Copyright (c) 2024 Valentin Goldité. All Rights Reserved.
from typing import Optional, Tuple
import torch
from torch import Tensor
def randomized_range_finder(
inputs: Tensor,
*,
size: int,
n_iter: int,
power_iteration_normalizer: str,
random_stat... |
53c07467cf265b7742b13d6b15a9e4b26e6d8740e1a9e508d78b08acac8d132b | Python | 1,629 | 48 | from typing import Tuple
from jaxtyping import PyTree
import jax
import jax.tree_util as jtu
import jax.flatten_util as jfu
import jax.tree_util as jtu
from jax.lax import with_sharding_constraint
from jax.sharding import PositionalSharding
import equinox as eqx
def tree_fully_flatten(tree: PyTree) -> jax.Array:
... |
5e5161bd5bc7a4cb920c8d1cf2f6dbe5d52cfe8014a4c20b4bc5c4209afa094b | Python | 1,629 | 58 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#... |
660c8b71ced60c6350535ced9c62f92294643a83c7dc8616820c495cb3e9b414 | Python | 1,629 | 62 | import lisa
from lisa import FromRegions, FromGenes, FromCoverage
import argparse
from lisa.cli.cli import oneshot_parser, multi_parser, regions_parser, coverage_parser
import argparse
import os
from argparse import HelpFormatter
from lisa.cli.cli import RstFormatter
from lisa.core.utils import Log
def new_format_help... |
50f8f292e8b8aaf9e539773ab4394aa3291563535467cd1dffcbe05903f7fb6f | Python | 1,630 | 55 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 1: simple network with one layer.
Simple network that consist of one analog layer. The network aims to learn
to sum all the elements from one... |
70f27df2097451c9d8e3c89f25ca508e08ab6d253ed079d0057a47e3a9e525df | Python | 1,630 | 33 | # Authentication error messages
TOKEN_AUTH_FIX_MESSAGE = (
"To connect to a cluster with token authentication, run `ray get-auth-token` "
"on the head node and copy the token to ~/.ray/auth_token on this machine, "
"or to a file that RAY_AUTH_TOKEN_PATH points to. If the cluster was started "
"with RAY_... |
953df9dffe1ca8e6986a5ee12abbd25260ad44b1bfb50eb0884c84e819c13e8c | Python | 1,632 | 43 | from tqdm import tqdm
from torch_pgn.train.train_utils import format_batch
import torch.nn.functional as F
import torch
def train(model, data_loader, loss_function, optimizer, scheduler,
train_args, epoch_num = 0, logger = None, writer = None, device='cpu'):
"""
Trains the model for an epoch.
:p... |
a8c269ed8991b8eb64efac6bb643619b31b455598ecab2d2d5e5520e837aafe9 | Python | 1,632 | 60 | #!/usr/bin/env python3
import os
import numpy as np
import tensorstore as ts
example_dir = os.path.abspath(os.path.dirname(__file__))
def write_single_res():
store = ts.open(
{
"driver": "zarr3",
"kvstore": {
"driver": "file",
"path": os.path.join... |
eab63dc7f964d9ff525ba1250248abbaa0e6dc49acf8d23ec583356e9208945d | Python | 1,632 | 57 | from abc import ABCMeta, abstractmethod
import numpy as np
class StepHook(object, metaclass=ABCMeta):
"""Hook function that will be called in training.
This class is for clarifying the interface required for Hook functions.
You don't need to inherit this class to define your own hooks. Any callable
... |
95688d034fa1b50bdb9e95cc57a1c153cde4d272e51eddda60b96260e863cfac | Python | 1,633 | 41 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
e536e1d1b78409abad79fde6ff947f3b59317e1790b70bfa65ff307aba839fde | Python | 1,633 | 58 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import torchvision.models as models
class VGG(nn.Module):
"""VGG/Perceptual Loss
Parameters
----------
conv_index : str
Convolutional layer in VGG model to use as perceptual output
"""
def __init__... |
0fc2977b1280e736ca81f27f0cd3dd6c4d558299404ac174eb34c28956d10b01 | Python | 1,635 | 53 | """
A collection of dictionary-based wrappers around the "vanilla" transforms for transformers functions
Class names are ended with 'd' to denote dictionary-based transforms.
"""
from monai.config import KeysCollection
from monai.transforms.compose import MapTransform
from src.transforms.transformer.array import Co... |
74d69550a920a7d61b60536f8ba2e15fbcc384eec09043a9676991bef32ffc87 | Python | 1,635 | 51 | import argparse
import tensorflow as tf
import importlib
import os, random
import json
import sys
import numpy as np
class project_params:
def __init__(self, params):
self.params = params
def main(project):
dataloader = selected_dataloader.dataloader_sleep_tfrecords(project)
train_dataset, val_dat... |
2ad54a1eac834ba2bfaa4812880c9d876132f1f98477d50c58a16ba6554784e6 | Python | 1,636 | 51 | from typing import Sequence, Union
import torch
from rising.random import AbstractParameter
from rising.transforms.abstract import BaseTransform, BaseTransformSeeded
from rising.transforms.functional.crop import center_crop, random_crop
__all__ = ["CenterCrop", "RandomCrop"]
class CenterCrop(BaseTransform):
de... |
4f4cc55cdde37637bfd1c31005d05d17972a092026cae8dcd608f1c19d8b29c8 | Python | 1,636 | 54 | import torch
from torch import nn
import tinycudann as tcnn
import numpy as np
class NGP(nn.Module):
def __init__(self, gray_act='Sigmoid'):
super().__init__()
self.gray_act = gray_act
scale = 0.5
L = 8; F = 2; log2_T = 10; N_min = 2
b = np.exp(np.log(20*scale/N_min)/(L-1))... |
73ba9be2e3a02683ee3140d096fcfaf01f43fefe58f0d34f6ac2bc92cfedae28 | Python | 1,640 | 58 | import base64
import json
import sys
import pytest
import ray
from ray._private.test_utils import (
wait_for_condition,
wait_for_dashboard_agent_available,
)
from ray.dashboard.tests.conftest import * # noqa
_RAY_EVENT_PORT = 12345
@pytest.fixture(scope="session")
def httpserver_listen_address():
retu... |
0bb63e979c8bc0c07ca9765f3fb380268892ae73cf3324b6f7d24a1c2f073a6a | Python | 1,641 | 56 | from typing import Optional, List
import numpy as np
from scipy import stats
from neuron_morphology.feature_extractor.data import Data
from neuron_morphology.features.statistics.coordinates import COORD_TYPE
from neuron_morphology.feature_extractor.marked_feature import marked
from neuron_morphology.feature_extracto... |
f8ad257efcd3e17f8ff697d241deb80ea8f98e461fc04e2fd9ff7c21a0540d8e | Python | 1,643 | 62 | #!/usr/bin/env python3
# Copyright 2004-present Facebook. All Rights Reserved.
import logging
import torch
def add_common_args(arg_parser):
arg_parser.add_argument(
"--debug",
dest="debug",
default=False,
action="store_true",
help="If set, debugging messages will be printe... |
5c421fb803592a47d54c0d44011057063d82d2e57f0b0098bbda847e8e6a9e06 | Python | 1,644 | 35 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
9047945b0caac41ebdb82cd642b6ae8a8afc35bba398e215e3cc35ef1995950a | Python | 1,644 | 53 | """
The purpose of this script is to initiate the main GUI
***
built as part of the Russell Ray Lab Breathing And Physiology Analysis Pipeline
***
Breathe Easy - an automated waveform analysis pipeline
Copyright (C) 2022
Savannah Lusk, Andersen Chang,
Avery Twitchell-Heyne, Shaun Fattig,
Christopher Scott Ward, Ru... |
91311585dfe05f747086ecdf05d04b5dd4b7de750e546d78a0ae0f799f8348e5 | Python | 1,644 | 43 | #usage: python _run-rnacontext-h3.py <model_res_10.txt> <nsites>
import sys,re,numpy as np
from mymo import util
mname=util.fullpath(sys.argv[1])
nsites=int(sys.argv[2])
table={}
def sumexp(v):return sum(np.exp(vi) for vi in v)
with open(mname) as m:
while True:
if "Base Parameters"==m.readline().strip():
... |
3de59eba0338608f1ec000cbaa2cc733dc5b19c4b450f30f9d9a84e1a9c4846a | Python | 1,646 | 50 | from dataclasses import dataclass
from typing import Any
import numpy as np
from .node import NIRNode
from .typing import Types
from .utils import calc_flatten_output, parse_shape_argument
@dataclass(eq=False)
class Flatten(NIRNode):
"""Flatten node.
This node flattens its input tensor.
input_type must... |
60a805a6ae55fd04d91603851d49d241635222c83d141dd2de3ff5886eaa446e | Python | 1,646 | 41 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
f1f42e8b71fd4aa24f534fa1a3b93ba9a3f171a73abe426d614b587ea61fef80 | Python | 1,646 | 43 | import nibabel as nib
import numpy as np
from nilearn.maskers import NiftiMasker
from numpy.testing import assert_array_almost_equal
from fmralign import metrics
def test_score_voxelwise():
A = np.asarray([[[[1, 1.2, 1, 1.2, 1]], [[1, 1, 1, 0.2, 1]], [[1, -1, 1, -1, 1]]]])
B = np.asarray([[[[0, 0.2, 0, 0.2, ... |
23fa52f2e1b3c9ee94cdf10db8b473d0f54643e60673ed05d8740732da423c99 | Python | 1,647 | 47 | import unittest
import os
import shutil
import tempfile
from neuron_morphology.morphology_builder import MorphologyBuilder
import neuron_morphology.swc_io as swcio
class TestSWCIO(unittest.TestCase):
def setUp(self):
data_dir = os.path.join(os.path.dirname(__file__), 'data')
self.swc_file = os.p... |
d4ff1bcde256c694634e00815633674a41da59ee80d3577f0d21178406eb1258 | Python | 1,647 | 45 | import unittest
import torch
from rising.transforms import ArgMax, OneHot, Permute
class TestChannel(unittest.TestCase):
def setUp(self) -> None:
self.batch_dict = {
"data": torch.arange(1, 10).reshape(1, 1, 3, 3).float(),
"seg": torch.rand(1, 1, 3, 3),
"label": torch... |
db66f49f5f9f908215618b83566f12eef889a1f0d5b87e6a3b71ed9c96b58710 | Python | 1,647 | 32 | from pandas import read_csv
from argparse import ArgumentParser
if __name__ == '__main__':
# Retrieve input data
parser = ArgumentParser()
parser.add_argument('--config_path', type=str, default='./Configurations.csv' , help='file with all considered configurations')
parser.add_argument('--retrieve... |
2b4974ba4bfb8d4d7acbf73d2a8ce17a32bca405973c4d3174aed2b1e1d20f3d | Python | 1,648 | 57 | import ast
import re
from pathlib import Path
REPO_ROOT = Path(__file__).absolute().parents[2]
LOG4J_ARTIFACTS = {
"log4j-api",
"log4j-core",
"log4j-slf4j-impl",
}
def _assignment_value(module: ast.Module, name: str):
for node in module.body:
if isinstance(node, ast.Assign):
for t... |
b613472fa8c18323719c2f1202cf4b9a54c65447d5dba705b7c66cce5237f3e5 | Python | 1,648 | 56 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import torch
def cg_change_mat(ang_mom: int, device: str = "cpu") -> torch.tensor:
if ang_mom not... |
3c04a9df6aab0d989867fb5fa57dfb0b59e0e1818b269fdcb996b88d801d7e4e | Python | 1,649 | 56 | # -*- coding: utf-8 -*-
"""
Created on Tue Dec 20 12:18:00 2022
@author: ju-bar
MTF file I/O
This code is part of the 'emilys' repository
https://github.com/ju-bar/emilys
published under the GNU General Publishing License, version 3
"""
import numpy as np
def read_mtf(file, debug=False):
"""
Reads radial ... |
afb7ca43220f358adf7686c57afe1262c5ea5005aa1c9813f60aef9ea09a373a | Python | 1,649 | 72 | import sys
from multicamera_acquisition.paths import DATA_DIR
from multicamera_acquisition.acquisition import acquire_video
import json
camera_list = [
{
"name": "Top",
"serial": 22181547,
"brand": "flir",
"gain": 3,
"gpu": 0,
"exposure_time": 4000,
"display... |
2ff7b3c9252d50413ae1cebbaf3a636e6ca0a1a867e21360271f39f70f405dc2 | Python | 1,652 | 46 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
c1f1cf00ff6ace1afa9e9c3bc4ecb1102f5834278af8f0ccec20ee41f795e553 | Python | 1,652 | 70 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Configurations for resistive processing units."""
from aihwkit.simulator.parameters import (
IOParameters,
IOParametersIRDropT,
UpdateParameters,... |
1defaba54724032a072922b4cc67f51ddb24ce3dcbf85aedd498c3a3b09664c0 | Python | 1,653 | 47 | # Ultralytics YOLO 🚀, GPL-3.0 license
from ultralytics.yolo.utils.checks import check_requirements, check_yaml
check_requirements('lap') # for linear_assignment
import torch
from ultralytics.yolo.utils import IterableSimpleNamespace, yaml_load
from .trackers import BOTSORT, BYTETracker
TRACKER_MAP = {'bytetrack... |
6b7c5da7c7d3c7847bd96e2ed38bb79c91bdc9b37901c1151578c5763651765a | Python | 1,653 | 44 | """Garbage-collection priority policy for the task-event store.
Each task event is assigned a priority tier. When the store is over capacity, events in
lower-priority tiers are evicted first: finished tasks first, then actor tasks, then
everything else.
"""
from ray.core.generated import gcs_pb2
from ray.core.generate... |
e76472a7ce7d16dd20c251566abe406565b1c2bee51abc245f6a47993208e703 | Python | 1,654 | 65 | # Copyright 2023 Google LLC
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
dce3ec104e2e8aa77899e67be166200402146add31d01186d2ef3675db7f1311 | Python | 1,655 | 61 | # __example_code_start__
from transformers import pipeline
from fastapi import FastAPI
import torch
from ray import serve
from ray.serve.handle import DeploymentHandle
app = FastAPI()
@serve.deployment(num_replicas=1)
@serve.ingress(app)
class APIIngress:
def __init__(self, distilbert_model_handle: DeploymentH... |
231d868e07d241aa47b0924eea4ebb39bd003ae4b4e2cf520f2eca4aa6799c00 | Python | 1,656 | 67 | """Generate binary PLY test fixtures from the ASCII cube definition."""
import pathlib
import struct
VERTICES = [
(-1.0, -1.0, -1.0),
(1.0, -1.0, -1.0),
(1.0, 1.0, -1.0),
(-1.0, 1.0, -1.0),
(-1.0, -1.0, 1.0),
(1.0, -1.0, 1.0),
(1.0, 1.0, 1.0),
(-1.0, 1.0, 1.0),
]
FACES = [
(0, 3, ... |
0c04ff1a0cb05d0431dc2a0902e2e378666dd5d3a344a68adb8c01d431362033 | Python | 1,657 | 52 | import torch
#model, alphabet = torch.hub.load("facebookresearch/esm:main", "esm2_t12_35M_UR50D")
import time
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import Dataset,DataLoader
import pandas as pd
from tqdm import tqdm
import torch
import esm
import numpy as np
from fairs... |
71f623e3fa2a8c42b5a36a77b653a3ea00c79695a5c455b591a76a1eade6ef7d | Python | 1,657 | 59 | from typing import Any, Dict, List
import ray
from ray.dag.dag_node import DAGNode
from ray.dag.format_utils import get_dag_node_str
from ray.util.annotations import DeveloperAPI
@DeveloperAPI
class FunctionNode(DAGNode):
"""Represents a bound task node in a Ray task DAG."""
def __init__(
self,
... |
8a942525e437f0501800ad7eb9e4827cac952d1d43c22494ca5e945ed1a00236 | Python | 1,657 | 33 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
0a0b1387807252a5076ee8c70572cb3adad451f7c34d79f40885f577f8985e1d | Python | 1,658 | 47 | import anndata
from .._registry import register_function
@register_function(
aliases=["批次效应校正", "batch_correction", "combat", "批次校正", "去批次效应"],
category="bulk",
description="Perform batch effect correction using ComBat algorithm for bulk RNA-seq data",
prerequisites={
'functions': [],
... |
4ed65e5350406bcee5dbbf62293db0d64ef291e7ddb7645ba8b261aeeeb9b311 | Python | 1,658 | 52 | from pathlib import Path
import numpy as np
from siapy.entities import SpectralImage
from siapy.transformations import corregistrator
from siapy.utils.plots import display_multiple_images_with_areas, pixels_select_lasso
# Set the path to the directory containing the data
# !! ADJUST THIS PATH TO YOUR DATA DIRECTORY ... |
08fe60d42f7c839cb936df6753f6bdb870b67f9bfa957194e0de68c961f0fde4 | Python | 1,659 | 64 | import numpy as np
from mozaik.connectors.modular import _lognormal_event_weight_sums
class ConstantDistribution:
def __init__(self, value):
self.value = value
def copy(self, seed):
return self
def next(self, n):
return np.zeros(n) + self.value
def test_lognormal_event_weight_... |
54435b357fa6b06aac04468ed54b8435ecdcefc51d1daae4c4e509d94dcaa2d8 | Python | 1,659 | 58 | import argparse
import pysam
def parse_arguments():
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input', required=True)
parser.add_argument('-o', '--output', required=True)
return parser.parse_args()
def truncate_cigar(cigars):
c = 0
new_cigars = []
for flag, n in cigars... |
9eb00ffe8ab87b3428b45ee2fea4aa3c174a2acd0655d30b501d542ba5547844 | Python | 1,659 | 39 | import matplotlib.pyplot as plt
import sys
import seaborn as sns
def main(argv):
sample = argv[0]
file="/Users/chaokuan-hao/Documents/Projects/PR_SpliceNN/results/800bp/"+sample+"/OUTPUT/SpliceAI_6_RB_p_n_nn_n1_TB_all_samples_thr_100_splitByChrom_L64_C16_L800_v21/BAM/"+sample+".discard.nh.txt"
cleaned_fi... |
1ab6f7ddc83e833c398cb42cfbde52788fd085a3d16a1c822268a420d2cbfadf | Python | 1,660 | 48 | from unittest import TestCase, skipIf
import subprocess as sp
import os
import tempfile
import shutil
import json
from dictdiffer import diff
class SnapPolygonsIntegration(TestCase):
@skipIf(
os.environ.get("TEST_INTEGRATION", "false") != "true",
"The integration tests can take a while - must op... |
53ea6b302986041927233a537b106fde782fa4e73ae59c0940226eb6f00a0379 | Python | 1,661 | 57 | #!/bin/python
#------------------- Description & Notes --------------------#
#------------------- Dependencies ---------------------------#
# Standard imports
import itertools
import functools
# Third-party imports
# Internal imports
from . import seq
#------------------- Constants ------------------------------#... |
ce63159d098bae6ca826c2e1fc1bcf1a7b6da2c845a071a40518d22f194b0b4e | Python | 1,661 | 66 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 31 17:01:28 2022
@author: saad
"""
import numpy as np
def rolling_window(array, window, time_axis=0):
"""
Make an ndarray with a rolling window of the last dimension
Parameters
----------
array : array_like
Array to add... |
69a127ad727a29f3257e8d6c9b5f6e398aeffc717cd517977b8f30801e8c0f0e | Python | 1,663 | 85 | # flake8: noqa
# __begin_untyped_builder__
# hello.py
from typing import Dict
from ray import serve
from ray.serve import Application
@serve.deployment
class HelloWorld:
def __init__(self, message: str):
self._message = message
print("Message:", self._message)
def __call__(self, request):
... |
06246fbdf52a26bceb3f511604ea97d50525b519470917287ddb7d7349d25c70 | Python | 1,665 | 60 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
For each resting-state scan for each subject ID, subtract mean BOLD timeseries
voxelwise.
Output:
demean_rfMRI_REST*_*.dtseries.nii Demeaned fMRI files.
Usage:
r_voxdemean.py <subject>
Arguments:
<subject> Subject ID
"""
import os
import numpy as np
i... |
311282019c48e502ba5cf403168565bb6dc47cee6275bbeecb4d1fb7371c15f8 | Python | 1,665 | 53 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
from copy import deepcopy
import pandas as pd
from matminer.featurizers.composition import ElementPrope... |
0a3754ea62da3c02cdb7bae5ab88effa6da2ff2e6ebd2cea30f367455dbf06c1 | Python | 1,666 | 46 | import torch
import torch.nn as nn
import torch.nn.functional as F
import DataSet
from Config import class_number
class TextRCNN(nn.Module):
def __init__(self,
vocab_size = len(DataSet.getTEXT().vocab), # 词典的大小(总共有多少个词语/字)
n_class = class_number, # 分类的类型
embed_... |
1e3cbae06e09f0cfb8cb995b5c27fc96b89e0a9fbf30d564c3fd8235f3e1444f | Python | 1,666 | 71 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
Simple classes for parsing and interpreting .fam files
"""
from collections import defaultdict
class Fam:
def __init__(self, samples, families):
self.samples = samples
self.families = families
class FamSample:
def __init__(self, family, I... |
97e166727ee8415a09644958b406118ea894b7ee9c596bdf0b6a445d7f864d7c | Python | 1,666 | 46 | #
# Copyright (c) 2023, NVIDIA CORPORATION.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... |
263a79efe93a612220865b37ac16defd1be64de04c65568bf2e4e410133521d2 | Python | 1,668 | 46 | '''
MIT License
Copyright (c) 2021 Deva Lab
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, publish, dist... |
956dcc9c30e45900bd71ac8a9f298e37968bf95757ca1e3db71e3c86613ec760 | Python | 1,668 | 63 | import numpy as np
import networkx as nx
import os.path
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter, MaxNLocator
import time
import math
import gc
gc.collect()
import warnings
import pysindy as ps # a library of sindy-2016
warnings.filterwarnings('ignore')
import os
... |
a6a83012ca5d0176e69615a40083846cb989a7f016b5779529cf84228c898691 | Python | 1,668 | 39 | import os
import json
import random
import uuid
import transforms3d
import numpy as np
import scipy.ndimage
from deepvoxnet2.components.sample import Sample
from deepvoxnet2.utilities import transformations
from tensorflow.keras.utils import to_categorical
from deepvoxnet2.components.transformers import Connection, Tra... |
31bde8c36279d7591f2268d6c45500ed4e7a9d5dfcc8e53cf1e501410bf615d4 | Python | 1,670 | 59 | import warnings
import argparse
import os
from os.path import join
from tqdm import tqdm
from glob import glob
from torchvision import transforms
import PIL
warnings.filterwarnings('ignore', category=UserWarning)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('inp', type=str, help='pa... |
3ac3f2ef26537e82dc558f5dba5eba6b60e216c17d06d2e96eb3a199fccf1ba6 | Python | 1,670 | 42 | import math
from functools import partial
import torch
from einops import rearrange
from .cauchy import cauchy_mult_torch, cauchy_mult_keops, cauchy_mult
from benchmark.utils import benchmark_all, benchmark_combined, benchmark_forward, benchmark_backward
def generate_data(batch_size, N, L, symmetric=True, device='... |
951a7dfe5d5fe3fcdff93bcec84d06cfb9c5c03d687f385583895fba9631e61e | Python | 1,670 | 46 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
ed1a3e2f35f12279ccd2302ca12828e4bd1a2343ad7d52f86a313b4a43e877a9 | Python | 1,672 | 54 | import os
import argparse
import pandas as pd
import numpy as np
from config import config
from utils import metadata_utils, coregister_utils
parser = argparse.ArgumentParser()
parser.add_argument('--split', type=int, default=1)
parser.add_argument('--split_num', type=int, default=1)
parser.add_argument('--start_idx... |
7969a1902c982caf7497ec91d8eff3289ab6d42a96acb6bf905b428f30214adc | Python | 1,674 | 66 | from __future__ import annotations
from collections import deque
from typing import TYPE_CHECKING, Any, Deque, Iterator, List, Optional
from typing_extensions import override
from .base import BaseBundleQueue
if TYPE_CHECKING:
from ray.data._internal.execution.interfaces import RefBundle
class FIFOBundleQueue... |
13c717c62aa214bdc48f09ccb4d0bae01f593061a2c9fc7a5e4c10af8e28770c | Python | 1,675 | 35 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
177f10c51f54f519c7dbb36ae648cb3ee0bdd5fc5cf5c22aa3df5b071f848376 | Python | 1,675 | 52 | import inspect
def is_cython(obj):
"""Check if an object is a Cython function or method"""
# TODO(suo): We could split these into two functions, one for Cython
# functions and another for Cython methods.
# TODO(suo): There doesn't appear to be a Cython function 'type' we can
# check against via i... |
e997946f52d26c00140f56694e058912881524c6eea64df2fd0af28ed68498e9 | Python | 1,675 | 35 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
1572ed1186251e019ecfbdca05647699ccd161ef275b935654d8df1ac8076ca2 | Python | 1,677 | 43 | import numpy as np
import pytest
from siapy.entities.pixels import Pixels
from siapy.transformations import corregistrator
from siapy.utils.plots import pixels_select_click # noqa: F401
@pytest.mark.manual
def test_pixels_select_click_manual(spectral_images, corresponding_pixels):
# image_vnir = spectral_images... |
fcacf07df5da3684490f9fb0af5b5789a27f7f67010caf2efad360ff2f08847c | Python | 1,677 | 35 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
b95f665e782d67d7a6d22b48655b75ae0461dfd096a1f70835a16890feb98b4e | Python | 1,678 | 47 | import numpy as np
import scipy.sparse as sp
import torch
import torch.utils.data as data_utils
class EdgeSampler(data_utils.Dataset):
"""Sample edges and non-edges uniformly from a graph.
Args:
A: adjacency matrix.
num_pos: number of edges per batch.
num_neg: number of non-edges per ... |
d20dd17cd2636003a8b74fa053dabccd2739eec75a096dee41f7801745c16fcf | Python | 1,678 | 40 | import pandas as pd
from sklearn.datasets import make_classification, make_regression
from siapy.features import (
AutoSpectralIndicesClassification,
AutoSpectralIndicesRegression,
)
from siapy.features.helpers import FeatureSelectorConfig
from siapy.features.spectral_indices import (
compute_spectral_indi... |
e5c89c7e7ac5d63603ab7884eaaaa5acb52e85312dec94c140274daaf46f2262 | Python | 1,678 | 54 | # fmt: off
# __doc_import_begin__
from ray import serve
from io import BytesIO
from PIL import Image
from starlette.requests import Request
from typing import Dict
import torch
from torchvision import transforms
from torchvision.models import resnet18
# __doc_import_end__
# fmt: on
# __doc_define_servable_begin__
@... |
64ce75fc3d004dbd7c0649365637bc88e30bb431446fae8d42a4cd1ac8b1ed35 | Python | 1,679 | 60 | # flake8: noqa
# fmt: off
# __step1_begin__
from ray import tune
import ray
import os
NUM_MODELS = 100
def train_model(config):
score = config["model_id"]
# Import model libraries, etc...
# Load data and train model code here...
# Return final stats. You can also return intermediate progress
# ... |
c1c56fbb644032a32b263300e44f48ad29b752905930a92bb59bf71e6b1a506f | Python | 1,679 | 22 | """Compare primitive kernels on identical historical states (no accumulated error)."""
import os,sys,json
from pathlib import Path
os.environ['TF_CPP_MIN_LOG_LEVEL']='2'
import numpy as np,tensorflow as tf
tf.config.threading.set_inter_op_parallelism_threads(1);tf.config.threading.set_intra_op_parallelism_threads(1)
p=... |
2f57871a8d4d1a20a47b4f1407420eec2672655fc2e65400cc572d4457ef8d63 | Python | 1,680 | 56 | # This Python file uses the following encoding: utf-8
"""
main program
***
built as part of the Russell Ray Lab Breathing And Physiology Analysis Pipeline
***
Breathe Easy - an automated waveform analysis pipeline
Copyright (C) 2022
Savannah Lusk, Andersen Chang,
Avery Twitchell-Heyne, Shaun Fattig,
Christopher Sc... |
f11d88e732f66a186f4e7698e7b07828456355e6096cdf333f1d1549054ac788 | Python | 1,680 | 45 | #!/usr/bin/env python3
# This script is used to zip a directory into a zip file.
# It only uses python standard library, so it can be portable and used in bazel.
import os
import os.path
import sys
import zipfile
# Everything in the zip file is stored with this timestamp.
# This makes the zip file building determini... |
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