sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
18ca46e8c9f59de3372775730d838886c9351eb2aae9d23e81c75106b90bb8e2 | Python | 5,485 | 134 | """
Tests for independence_tests.py.
"""
from __future__ import print_function
from collections import OrderedDict
import numpy as np
import pytest
import sys
import tigramite.data_processing as pp
from tigramite.toymodels import structural_causal_processes as toys
# Pylint settings
# pylint: disable=redefined-outer-... |
7589434717486dca50d0eab69e55f4e24597b1102e310aa111973df2b0853068 | Python | 5,486 | 191 | # amplifier.py
# Copyright (C) 2013 Bastian Venthur
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program ... |
f65c0e3282e20a4fca6b5f9f939266df61450bc47d353d65cf8a2d7d39c2f9a3 | Python | 5,486 | 135 | import numpy as np
import pytest
from hypothesis import given, settings
from hypothesis import strategies as st
import seqpro as sp
from seqpro import AA # standard AminoAlphabet
from seqpro.rag import Ragged
def _bio_like_translate(seq_str: str) -> str:
"""Reference using AA.codon_to_aa directly (independent o... |
914a2c9508577b51d33c665bce8ef8e130717835856fe4d6955a1cdc9725f706 | Python | 5,487 | 135 | """Belief propagation to compute the marginal probabilities of a spot being
occupied by a cell.
"""
from typing import Optional
import cv2
import numpy as np
from ..configuration import config
from . import utils
def create_neighbor_offsets(neighborhood: np.ndarray) -> np.ndarray:
"""Helper function to convert ... |
e89e66339e65d8bde7b6d30a68323958531c09ef89a6a030dbe1432a3c3e83af | Python | 5,487 | 126 | """Implementation of a space that represents finite-length sequences."""
from collections.abc import Sequence as CollectionSequence
from typing import Any, List, Optional, Tuple, Union
import numpy as np
import gym
from gym.spaces.space import Space
class Sequence(Space[Tuple]):
r"""This space represent sets of... |
1381b7cadca2887fb0834a7b8138599005ddd537350341f9b44e3fd036870e65 | Python | 5,488 | 139 | import itertools
import json
import os
import re
from json import JSONDecodeError
from typing import Iterable
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.axes import Axes
from angorapy.common.const import PATH_TO_EXPERIMENTS, BASE_SAVE_PATH, QUALITATIVE_COLOR_PALETTE
matplotl... |
1b5ec3d722747e2ff8645a2465493f6a6d1803c16bafc24d7cc70add8325fc63 | Python | 5,488 | 155 | # Copyright 2022 Deepfold Team
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... |
7021cf1c696b173d4cf1e24242c239412234639c254e10521c9cf02ef453a92e | Python | 5,488 | 139 | """MSCOCO Semantic Segmentation pretraining for VOC."""
import os
import pickle
from tqdm import trange
from PIL import Image
import numpy as np
from .utils import try_import_pycocotools
from ..segbase import SegmentationDataset
class COCOSegmentation(SegmentationDataset):
"""COCO Semantic Segmentation Dataset fo... |
23a37f098e8be7e3293c35b8189a19600b07701ddee866a33b0495a91466c3f9 | Python | 5,491 | 141 | #!/usr/bin/env python3
"""
Test script for the new unified backup status endpoint.
This script tests the modified backup status API that combines information
from both MySQL backup daemon (port 8090) and rsync backup daemon (port 8093).
"""
import json
import urllib.error
import urllib.request
def test_individual_s... |
545e77ad9a3be2603bbbab18bfb6d450760fe2d4767a98173d3f850d79476ff4 | Python | 5,491 | 163 | """Compatibility checks for tensors saved into portable bundles.
This module codifies which tensor layouts and dtypes the portable bundle path
accepts in this sprint. Save code calls these helpers to decide whether a
tensor should be written, skipped under ``strict=False``, or rejected with a
hard ``TorchLensIOError``... |
c408a0699c9ea668f4dcf1eef27174cd840f8918ed7761946d39aa447e5772f6 | Python | 5,491 | 161 | # Mossy layer at 45, 90, 135 degrees
from os.path import join
import numpy as np
import os
import pandas as pd
from library.comput_utils import cal_hd_np
from library.utils import save_pickle
from library.simulation import simulate_SNN
# # ================================= Network Parameters ========================... |
0adbdc0e0fe98c9d991d63e7613240e971555f9abc442d010d12308ffb38feed | Python | 5,492 | 162 | import pytest
import numpy as np
from BM3D.src.support_function import *
# The test function takes in a function to test and the expected output
def test_initialization():
Img = np.random.rand(10, 10)
BlockSize = 3
Kaiser_Window_beta = 2.0
# Invoke the function being tested
init_img, init_weights,... |
36c57db5fb8acc90ed99db28bd9010bda527871ad91205ccf8d039a7e5cd3775 | Python | 5,492 | 118 | from ovseg.model.SegmentationEnsemble import SegmentationEnsemble
from ovseg.model.SegmentationModelV2 import SegmentationModelV2
from ovseg.data.Dataset import raw_Dataset
from os.path import join, exists
from os import environ
import torch
import numpy as np
class SegmentationEnsembleV2(SegmentationEnsemble):
... |
61d3d35f01f62c083fd9eee538fd5c1ef655da5648bc050999a115666f77deb3 | Python | 5,494 | 124 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
""" Utility functions """
import os
import sys
import math
import random
import numpy as np
from datetime import datetime
from sklearn.metrics import auc, roc_auc_score
from scipy.stats import pearsonr, spearmanr, t
import torch
import torch.nn ... |
8a295992cf30dda5624cee883c64e38b40548bd123bb06a65edf44105bf3cb71 | Python | 5,494 | 149 | """B11 (cone preflight, exact-membership oracle) + B12 (generated cache key).
B11's oracle is EXACT (memo D-12 / composition row "preflight x lane"):
predicted replay membership EQUALS the engine's actual recomputed cone.
B12 pins the generated-universe property the warm-cache key now has: every
capture option is in t... |
973d74c9cfe09b92b12670e9b923110e4fb6652f9c6caa82b11de52feac2c0d8 | Python | 5,495 | 166 | #!/usr/bin/env python
#
# Copyright 2009, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
bfea54394e1a1401a1dddfb31c134d772c337801080a3e417a55c675e169f557 | Python | 5,495 | 160 | import dash
import dash_core_components as dcc
import dash_html_components as html
from dash.dependencies import Input, Output
import numpy as np
from spitfire.chemistry.flamelet import Flamelet
from spitfire.chemistry.mechanism import ChemicalMechanismSpec
m = ChemicalMechanismSpec(cantera_xml='heptane-liu-hewson-che... |
4870a73b8cf7639afca85c05215af65265df0247da3fd08b0ee204b8192d0505 | Python | 5,497 | 153 | import os
import pandas
import pandas as pd
import torch
from hydra import initialize, compose
from matplotlib import pyplot as plt
from torchmetrics.utilities.compute import auc
from data.loader import get_kfold_dataloader3d
from initial_setting import get_instance
from utils.calculate import margin_of_error
def i... |
833af9e9502657c2239b5860ceb5bc01826659011036dde9d6514fd657c71662 | Python | 5,498 | 168 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
8dd7481d9efd3ebe4a7d58e24be6bf73c33db4df5a29cda518e9bed1f154345e | Python | 5,498 | 144 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: Pramod Bharadwaj Chandrashekar
@email: pchandrashe3@wisc.edu
"""
import math
import torch
from torch import nn
import torch.nn.functional as F
class FNN(nn.Module):
""" Class for Feed Forward Network"""
def __init__(self, input_dim, hidden_dim_array,... |
46734f82943943ade2a667972a3c94e77147cdea7624e86fc1688913940ed1ee | Python | 5,500 | 129 | """r-b4 R29-2: input alias validation pre-filters pairs with an interval sweep.
``_record_unpreserved_tensor_aliases`` ran the exact ``touched_bytes_relation``
ladder on EVERY pair -- O(T^2) in tensor-leaf count (measured 0.72 s at 4k
disjoint leaves). The sweep (``_alias_candidate_pairs``) drops only pairs the
ladder... |
c6f00ba1a4c6d4e0cc5ad582b689a0451ee259272e0d60492264a46bfd9c6798 | Python | 5,501 | 146 | import pytest
import torch
import torch.nn as nn
from pytest_mock import MockerFixture
from torch import Tensor
from torch import distributed as dist
from torch.nn import Module
from lightly.loss.barlow_twins_loss import BarlowTwinsLoss
from tests.ddp_helpers import NUM_PROCESSES, USE_PYTEST_POOL
class BarlowTwinsLo... |
0764063b5e426878d2fb38b7011998cd90ee25edd04ee737a929f624f0e5cd9f | Python | 5,502 | 133 | import torch
import torch.nn as nn
from torch.autograd import Variable
from collections import OrderedDict
import numpy as np
def summary(model, input_size, batch_size=-1, device="cuda"):
def register_hook(module):
def hook(module, input, output):
class_name = str(module.__class__).split(".... |
76dca60ba87a712719151a465016e210e397eeab67ad014368cdf9a067fd1c37 | Python | 5,502 | 175 | from __future__ import annotations
from abc import ABC, abstractmethod
from typing import Iterable, TypeVar, Generic
import warnings
import torch.nn as nn
_T = TypeVar("_T")
class Domain(nn.Module, ABC, Generic[_T]):
"""Base class for stimulus domain.
This class is used to convert data between each domain... |
c7b7fd630b47158e3faae7eb442f9bfb7a1d09caba46a32dd9b7112e93fadc70 | Python | 5,503 | 147 | # This example requires the following dependencies to be installed:
# pip install "lightly[timm]"
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU: fewer clusters, a shal... |
b66489b17f1e574ba1895025078a6aaf516778faf8d9139c3b4794a0dbd7135b | Python | 5,504 | 209 | from typing import cast
import numpy as np
from numpy.typing import NDArray
from ._utils import SeqType, cast_seqs, check_axes
from .alphabets._alphabets import NucleotideAlphabet
def length(seqs: SeqType, length_axis: int | None = None) -> NDArray[np.integer]:
"""Calculate the length of each sequence.
Par... |
f5a76ac1ca28ab438bfd0ddcf3e93e114bc1c72d8ed0c94ed075707bdea25263 | Python | 5,504 | 188 | from collections.abc import Mapping
from enum import Enum
from textwrap import dedent
import networkx as nx
import numpy as np
from anndata import AnnData
from matplotlib import axes
from matplotlib.axes import Axes
class Empty(Enum):
token = 0
_empty = Empty.token
class _AxesSubplot(Axes, axes.SubplotBase):... |
8e58d40a29332b2d74ae9b91ad5335c5a74dbcf7967c017fe53a787a0beaa38c | Python | 5,506 | 156 | import os
import numpy as np
import rclpy
from rclpy.node import Node
from rclpy.parameter import Parameter
from std_msgs.msg import Bool, String, Int32, Float32MultiArray, MultiArrayDimension
from camera_code import Camera
class CameraROS2Node(Node):
def __init__(self):
'''
Initialize the CameraR... |
e8d28d6ff1979274c3cd4547fb1ccfcd11cc70c7341499c2ae05a5cde7e3e2c0 | Python | 5,506 | 182 | """
helper_fcts.py
This script contains helper functions for paper analysis plotting.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
from pathlib import Path
from util import file_util, logger_util
TAB = " "
logger = logger_util.get_module_logger(name=__name__)
##########... |
f5fe8e1bb8865248054c4b6401b188d981f567f717f4335e59c27f7ace8b1fe9 | Python | 5,508 | 182 | import pytorch_lightning as pl
import torch
from survival_plus_x.models.mae import MAE
class MAELightning(pl.LightningModule):
def __init__(self,
vit,
learning_rate,
masking_ratio,
decoder_dim,
decoder_depth,
... |
c4fa810b52cd389efe2149ff2677c8ac27c84b95597258cdf6c69a665758a2a0 | Python | 5,509 | 143 | from typing import Optional
import numpy as np
from anndata import AnnData
from ..._compat import Literal
import scipy.spatial as spatial
from tqdm import tqdm
_SIMILARITY_MATRIX = Literal["cosine", "euclidean", "pearson", "spearman"]
def adjust(
adata: AnnData,
use_data: str = "X_pca",
radius: float = 5... |
122bb5ea90b6d374403fe75478991eb45de0399c89d7478302d4c7414dcf6b49 | Python | 5,510 | 164 | """This module controls the pynapple configurations.
## Backend configuration
By default, pynapple core functions are compiled with [Numba](https://numba.pydata.org/).
It is possible to change the backend to [Jax](https://jax.readthedocs.io/en/latest/index.html)
through the [pynajax package](https://github.com/pynapp... |
921a967d960504b29cccf807c5b6a062b84d7081e19fe6b9fb7c24fbbc6987e4 | Python | 5,510 | 149 | # SOURCE: vendored from autonlab/auton-survival @ 5dde465f7223601717abddc1d075e837707c403b
# https://raw.githubusercontent.com/autonlab/auton-survival/5dde465f7223601717abddc1d075e837707c403b/auton_survival/models/dcm/dcm_torch.py
# https://raw.githubusercontent.com/autonlab/auton-survival/5dde465f7223601717abddc1d075e... |
eb0dfc5047883f75afbb53871dc3d054edce30b821b2920db9f49b7d4ef9b5f8 | Python | 5,510 | 164 | import pre_process
import os
import data_prep
import numpy as np
import scipy
from scipy.stats import pearsonr, spearmanr
import matplotlib.pyplot as plt
import tensorflow as tf
import numpy as np
import pandas as pd
import tensorflow.keras.backend as K
from sklearn.model_selection import train_test_split
from sklearn ... |
2360b1d697a4def3f8111707bfcc31c091efee4d578785b103a037794415104a | Python | 5,511 | 181 | import sqlite3
import pandas as pd
import json
def get_queries():
CONFIGPATH = './configs/visualization.sql.json'
with open(CONFIGPATH, 'r') as f:
queries = json.load(f)
return queries
def get_generic_query_result(db_uri, queryid, return_csv=True):
queries = get_queries()
query = querie... |
3e6bbfacc46d453f3d75cca2d55f7bf961ae5ff21c64120c9f8cecef62d60c04 | Python | 5,511 | 163 | """Mask transformation functions."""
import copy
import numpy as np
from PIL import Image
from ..mscoco.utils import try_import_pycocotools
__all__ = ['flip', 'resize', 'to_mask', 'fill']
def flip(polys, size, flip_x=False, flip_y=False):
"""Flip polygons according to image flipping directions.
Parameters... |
0b6efcf9678aad11b0db790415567a3cc72c9f89d8084a8d52822e865c92e07c | Python | 5,512 | 137 | """
BASIL GUI for Oxford ASL - Structural data options
Copyright (C) 2020 University of Oxford
"""
import wx
import wx.grid
from .widgets import TabPage
class StructureTab(TabPage):
"""
Tab page containing options for structural space transformation
"""
EXISTING_FSLANAT = 0
NEW_FSLANAT = 1
I... |
c39e0f78c23c84454d25b85485d74422d1051e26373b4325eb6138456f5d2629 | Python | 5,513 | 125 | """
Check the first value of every ABF to ensure it matches what we expect.
"""
import sys
from numpy.testing import assert_almost_equal
import pytest
import datetime
import inspect
import numpy as np
import glob
try:
# this ensures pyABF is imported from this specific path
sys.path.insert(0, "src")
impor... |
f8d63bf488f4548793fa0fda9b9c37b70c37199bd76e7d5653a0230b3b8b436a | Python | 5,513 | 180 | import numpy as np
from numpy.random import default_rng
import pathlib
from mpi4py import MPI
from causal_optoconnectics.tools import conditional_probability, joint_probability, roll_pad
from causal_optoconnectics.generator import (
construct_connectivity_filters,
simulate,
construct_input_filters,
gen... |
ff82d81b454b4b3972e611793f330694de247f2386122ae251288f5ba42f268b | Python | 5,514 | 142 | # -*- coding: utf-8 -*-
"""
To explore the time fluctuation of the network
clean the data preprocessed from frmriprep
extract the data using yeo7 network
calculate the correlations between each session with average seesion
By M.-Y. Wang 10-Jul-2023
"""
import os
from nilearn import datasets
from nile... |
13af813e241323f6f690f9b1d2effa1ed44ae24ebce37dd80f67000427084a0b | Python | 5,517 | 125 |
"""
BASIL GUI for Oxford ASL - Calibration options
Copyright (C) 2020 University of Oxford
"""
from .widgets import TabPage
# T1 and T2 defaults for different reference tissue types
REF_TISSUE_DEFAULTS = {
"csf" : (4.3, 750),
"wm" : (1.0, 50),
"gm" : (1.3, 100),
}
class CalibTab(TabPage):
"""
Ta... |
2528962205737319054434337d224976a6b8389a5852eba60942bc95bc9aab5d | Python | 5,517 | 178 | from typing import List, Tuple, Dict, Union, Optional
from pathlib import Path
import pandas as pd
import torch
from torch_geometric.loader import DataLoader
import torch_geometric.transforms as T
from coeffnet.dataset.reaction import ReactionDataset
from utils import (
get_train_data_path,
get_validation_... |
a8c84f8d69f0f6a2c4817d51737b02b155a48eeba7d07cc2b9e8dac5c5f49f22 | Python | 5,518 | 132 | """
This script shows the training pipeline for k-fold training, without logging it via wandb.
"""
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
from sklearn.model_selection import StratifiedKFold
from tf_spiking.helper import TrainingHistory
from tf_spiking import DenseLIF, ... |
c569f25b0681a2d99c7c5248bcea351b83bcd2ea2f43b64f5eefc89294de1bc9 | Python | 5,518 | 169 | import argparse
from . import gaussian_diffusion as gd
from .respace import SpacedDiffusion, space_timesteps
from .unet import UNetModel
def create_model_and_diffusion(cfg):
model = create_model(
image_size=cfg.TRAIN.IMG_SIZE,
num_classes=cfg.TRAIN.NUM_CLASSES,
num_channels=cfg.TRAIN.NUM_... |
f1c171e0dca8e6d9630ef357099088d2ab46fd813a39ca4fa233591fb53e4fee | Python | 5,519 | 155 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
72819eb9bd02a2a7ad4dea25aa748baf96b973febe99230e579e38f8222389f0 | Python | 5,523 | 149 | import os
import random
import re
import tempfile
import unittest
import hydra
import torchvision
import yaml
from hydra.experimental import compose
try:
from hydra import initialize
except ImportError:
from hydra.experimental import initialize
import lightly
from lightly.data import LightlyDataset
from ligh... |
90c60216e357c417cd7855deb693138c0fb5f37485d4d18b500a835dc69bcfb3 | Python | 5,525 | 189 | """TensorFlow payload codec and portable ``.tlspec`` round-trip tests."""
from __future__ import annotations
import json
from pathlib import Path
from typing import Any
import numpy as np
import pytest
import safetensors # noqa: F401
from conftest import tensorflow_backend_modules
tf, keras, _TF_BACKEND_SKIP_REASO... |
f0228e5a7b46a4d1d8a6324068f71ba433ce9de1b97c4d4fc5a73d4890a381fc | Python | 5,525 | 141 | """SQLAlchemy session."""
import time
from kombu.utils.compat import register_after_fork
from sqlalchemy import create_engine, inspect, text
from sqlalchemy.exc import DatabaseError
from sqlalchemy.orm import sessionmaker
from sqlalchemy.pool import NullPool
from celery.utils.log import get_logger
from celery.utils.t... |
7ec8748a462641e2291eb1c5f408b70fa2e65a42410298cbbf0144cef19a19ab | Python | 5,526 | 155 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
894f0ca9f9caef3841494a0bce2ab63b584df333054328c4d02c98b5e355e8c6 | Python | 5,526 | 141 | """Tests for the xcp_d.utils.write_save module."""
import os
import numpy as np
import pytest
from xcp_d.utils import write_save
def test_read_ndata(ds001419_data):
"""Test write_save.read_ndata."""
# Try to load a gifti
gifti_file = ds001419_data['gifti_file']
with pytest.raises(ValueError, match=... |
8b45e202eb4d6a5f489801aa32d48b544abf422a99a06025016c25486acd63c4 | Python | 5,526 | 153 | #!/usr/bin/env python3
# coding: utf-8
"""
Created in April 2022
@author: Simon Delarue <sdelarue@enst.fr>
"""
from typing import Optional, Union
import numpy as np
from scipy import sparse
from sknetwork.gnn.activation import BaseActivation
from sknetwork.gnn.loss import BaseLoss
from sknetwork.gnn.base_layer import... |
22ef9a0063f203798482262abbdeff15def815858184a0379f90c32a9b056c34 | Python | 5,528 | 184 | from unittest.mock import Mock, patch
import pytest
from celery import chord, group
from celery.app import builtins
from celery.contrib.testing.mocks import ContextMock
from celery.utils.functional import pass1
class BuiltinsCase:
def setup_method(self):
@self.app.task(shared=False)
def xsum(x)... |
b2dc276cd9c2893323838f9910eebed5717d5e9bb32485c9537216ce42cf72e7 | Python | 5,530 | 160 | """Scheduler for Python functions.
.. note::
This is used for the thread-based worker only,
not for amqp/redis/sqs/qpid where :mod:`kombu.asynchronous.timer` is used.
"""
import os
import sys
import threading
from itertools import count
from threading import TIMEOUT_MAX as THREAD_TIMEOUT_MAX
from time import s... |
a9bc4fd3b055b08e8c2b87ff36021588919127d50e9cf59df8162b124e8e648b | Python | 5,532 | 173 | """
sess_file_util.py
This module contains functions for loading and reading from data
files generated by the Allen Institute OpenScope experiments for the Credit
Assignment Project.
Authors: Colleen Gillon, Blake Richards
Date: August, 2018
Note: this code uses python 3.7.
"""
import glob
from pathlib import P... |
1ce7ff52176524cf9bdc11ecff9732de236dfe1e3e197eb25d382e3509328712 | Python | 5,533 | 166 | # This example requires the following dependencies to be installed:
# pip install lightly
# pip install "scikit-learn>=1.7.1"
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single... |
0603c7acfb570cd6ec172317e40cd3c06d8c186eee64a7a576d2b34522c604f4 | Python | 5,534 | 174 | # %%
import pandas as pd
import matplotlib.pyplot as plt
from globals import path, sessions, subjects, folder_spots_noboth, colours_types
import os
from plotting import prettifySpinesTicks, removeSpines
lwD = 7
widthtick = 10
lenD = 20
ss = 50
transparency = 0.9
mc = "black"
plt.rcParams.update(
{
"font.s... |
8d6bf870e6e6042a398d13543f40468913ce008e35d44399a838f16ae6008cdd | Python | 5,534 | 149 | #!/usr/bin/env python
"""
Using a pre-trained model, and given the preprocessed signal arrays,
annotate the state for each sample in the signal array, and save out a
1) a hypnogram, and
2) the likelihood of the predicted state for each sample.
The latter can then be used to manually refine annotation.
"""
import nump... |
f2660d4395141c7671559300b5c6216f367dbe9e0002afd6f1e35fd47923dd69 | Python | 5,534 | 148 | """Semantic identity goldens for the RenderIR-backed rank renderer.
Regenerate deliberately with ``TORCHLENS_UPDATE_RANK_RENDER_IR=1`` (the
update run reports SKIP, never green; re-run without the flag to verify).
Governance adjudication (b10 R78 round-3): this family is ENVIRONMENT-
SENSITIVE — the semantic record i... |
87b872e1f26e87a880c0c42e35cbc32d1cd4e49123265f7435e8879317c3993f | Python | 5,537 | 155 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
7a9e0a0359a529f29e4531b51d5d44eda9ee01634d6e6a575a67bc6fff527ebf | Python | 5,538 | 165 | #!/usr/bin/env python
import sys
import tarfile
import unicodedata
import wave
from glob import glob
from os import makedirs, path, remove, rmdir
import pandas
from sox import Transformer
from tensorflow.python.platform import gfile
from deepspeech_training.util.downloader import maybe_download
from deepspeech_traini... |
7ced5965cdc21bc513cd394edf50bf0414aef8df49ff83d0210da736048c4a86 | Python | 5,538 | 179 | """Smoke tests for garbage-collected results on the Redis result backend.
Regression coverage for #10326: the garbage collector can run
``AsyncResult.__del__`` -> ``cancel_for`` while the same thread is in the
middle of a pubsub SUBSCRIBE, UNSUBSCRIBE or ``get_message()``. The nested
UNSUBSCRIBE deadlocked on redis-p... |
ff5fc2de58486fb9d0f944585ff2ae3a1234ba1f0689ccb84d14d17964ab9799 | Python | 5,539 | 150 | """Calculate Intersection-Over-Union(IOU) of two bounding boxes."""
from __future__ import division
import numpy as np
def bbox_iou(bbox_a, bbox_b, offset=0):
"""Calculate Intersection-Over-Union(IOU) of two bounding boxes.
Parameters
----------
bbox_a : numpy.ndarray
An ndarray with shape :... |
8d47fae7b594cb94f450ca77bd8374be0027db3384a3bedd4a815e7b5a44d22d | Python | 5,540 | 154 | from typing import Callable, Dict, Hashable, Optional
import networkx as nx
import numpy as np
from nfp.frameworks import tf
from nfp.preprocessing import features
from nfp.preprocessing.preprocessor import Preprocessor
from nfp.preprocessing.tokenizer import Tokenizer
try:
import rdkit.Chem
except ImportError:
... |
9fae56aa56abcf0f780297af8af77af2bfe82c0f6c4c52d6fbc9f8582e6bd8c3 | Python | 5,540 | 125 | import copy
import os
import warnings
from typing import Any
from xml.etree import ElementTree as ElemTree
from mirp.settings.utilities import str2list, str2type, read_node
def import_data_settings(
path: str,
is_mask: bool
) -> list[dict[str, Any]]:
if not os.path.exists(path):
raise ValueError(... |
4f8aa4518fd602c40f5cff2a1a7f60423e1774e7d5db1602f50f52f0d91659b6 | Python | 5,543 | 229 | import array
import pytest
import struct
import sys
import rpy2.rinterface as ri
try:
import numpy
has_numpy = True
except ImportError:
has_numpy = False
ri.initr()
def test_init_from_iter():
seq = range(3)
v = ri.IntSexpVector(seq)
assert len(v) == 3
for x, y in zip(seq, v):
ass... |
94b7d92b748d24c23ff32860768549dd4962e0697da951eb89098edc827f46f6 | Python | 5,543 | 162 | """TensorFlow static FuncGraph fallback tests."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import numpy as np
import pytest
from conftest import tensorflow_backend_modules
import torchlens as tl
from torchlens.backends.tf import TFBackend
tf, keras, _TF_BACKEND_SKIP_REASON... |
fef371a3921bde31779642895681859f7d73353b94be79b475f21b12746dadf6 | Python | 5,543 | 166 | """Medians of SPD/HPD matrices."""
import warnings
import numpy as np
from .base import sqrtm, invsqrtm, logm, expm
from .distance import distance
from .mean import mean_euclid
from .utils import check_weights
def median_euclid(X, *, tol=10e-6, maxiter=50, init=None, weights=None):
r"""Euclidean geometric media... |
dcba5cf90b6fd53f59abda2dfd854c785cca42464c4fe027dae205d39d6cb14d | Python | 5,544 | 121 | import torch
import torch.nn as nn
from torch.autograd import Variable
import torch.nn.functional as F
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import Dataset, DataLoader
from torch.autograd import Variable
from torch.nn import Linear, ReLU, CrossEntropyLoss, Sequential, Conv... |
e28a0434cd4e633e9b9596e926501030185bd862702342b9e9bef9b336cf1dbd | Python | 5,544 | 171 | """Shared application unit-test support for job runners."""
import datetime
import os
import tempfile
import time
from galaxy import model
from galaxy.jobs.job_destination import JobDestination
from galaxy.util import bunch
class MockJobWrapper:
"""A runner-facing ``MinimalJobWrapper`` test double with real wor... |
0caab340533e119a65db5acceca2d01687828005f819da4744cc114c098b4ba0 | Python | 5,545 | 142 | from typing import Optional, Tuple, Union
import torch
from pytorch_lightning import Callback, LightningModule, Trainer
from pytorch_lightning.accelerators import Accelerator
from torch import Tensor
from torch.nn import functional as F
class KNNOnlineEvaluator(Callback):
"""Weighted KNN online evaluator for sel... |
1b0dc600a6cee976fae83f718c60a3384c9b34fdfa5b77369bd0a7556acf03c7 | Python | 5,545 | 194 | """Set of Error classes for gym."""
import warnings
class Error(Exception):
"""Error superclass."""
# Local errors
class Unregistered(Error):
"""Raised when the user requests an item from the registry that does not actually exist."""
class UnregisteredEnv(Unregistered):
"""Raised when the user reque... |
d1b4f3a3d4efb98329cfe96b2cd4853da1b259f1ae062d7ddd346fc7147ff5c8 | Python | 5,545 | 171 | import numpy as np
import skimage.io
from scipy.ndimage import zoom
from skimage.transform import resize
from caffe.proto import caffe_pb2
def load_image(filename, color=True):
"""
Load an image converting from grayscale or alpha as needed.
Take
filename: string
color: flag for color format. Tru... |
f7b7c7775fffe2863af8d894bfc46069b63b74c942e28bacb6990ef0e05f3227 | Python | 5,545 | 117 | from nose import tools as nt
from nose.tools import assert_dict_equal
import neurom
from neurom import load_neurons
import numpy as np
from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_equal, assert_raises
from tns import extract_input
import os
import json
from tns import TNSError
import... |
0b7eb1c5201508cc81df74d315eee5fe8d37f6c7f6142bb81871606d7b3324a1 | Python | 5,547 | 144 | #!/usr/bin/env python3
"""Cross-paper consistency check.
Run one canonical synthetic subject through every paper's *canonical* compute
path and assert byte-identical 5D output. Catches the kind of cross-paper drift
the May 2026 audit found (paper 5 / paper 6 / paper 7 had different generations
of `compute_phi_5d` scat... |
cfd2cde87a2d6b5081d199b4301412296901489019d7aaa191779844e8200a2b | Python | 5,547 | 111 | import torch
class _input:
""" Algorithm input.
"""
def __init__(self):
self.dat = None
self.dim = None
self.ct = None
self.mat = None
self.mu = 1.0
self.po = None
self.sd = 1.0
self.tau = 1.0
self.file = None
self.fname = No... |
b0cfb99c3a278d4dc3d5615bc79a50a4c1bbb87e39d17a1e6799501b880f07b0 | Python | 5,548 | 165 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import argparse
from sklearn.model_selection import LeaveOneOut
from sklearn.model_selection import train_test_split
from models import GraphConv, AE, LP
from utils import *
parser = argparse.ArgumentParser()
parser.add_argument('--n... |
d2c94ddcd9bc1be00b4247ae396a5b32326647011d3be700f2d5725469328e0d | Python | 5,548 | 158 | #!/usr/bin/env python3
"""
File: save_ieqtl_fdr_matrix.py
Created: 2022/07/05
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source tree.
... |
ed9715dfe3443dd09e10055055d57fe69fd644e2a36fe1c7640fc298feab93c5 | Python | 5,548 | 149 | import numpy as np
from numpy.testing import assert_array_equal
import pytest
from pyriemann.datasets import sample_gaussian, RandomOverSampler
from pyriemann.geometry.distance import distance_riemann
from pyriemann.geometry.test import (
is_herm_pos_def as is_hpd,
is_real,
)
pytestmark = pytest.mark.numpy_on... |
ed0e1a73890422f97bca08dee32982a700e51454b5b9ed4708ebc02ccf79cc6f | Python | 5,549 | 156 | """ Code to fine-tune hugging-face implementation of GPT2 model.
https://huggingface.co/
"""
import warnings
warnings.simplefilter(action="ignore")
import os
import gc
import glob
import logging
import argparse
import pandas as pd
from transformers import GPT2LMHeadModel, GPT2Tokenizer
from irnlm.models.tokenizer i... |
fc6120dd76a8eefae73cd6a0ae846459305171b7faf1c5c3941ae3170d0b0bc7 | Python | 5,549 | 129 | import numpy as np
import math
import random
from collections import defaultdict
def tokenize_pet_mlm_txt(tokenizer, config, txt1, txt2, txt3, txt_trim, mask_idx=None):
'''
Tokenizes the text by trimming the appropriate txt
:param tokenizer:
param config:
:param txt1:
:param txt2:
:param ... |
7f72a640ad0edc4403b3d3f2cb21d12c4ea1a9a9c003f064cd028f85c5efba07 | Python | 5,550 | 172 | #!/usr/bin/env python
"""
NAME : LDC TIMIT Dataset
URL : https://catalog.ldc.upenn.edu/ldc93s1
HOURS : 5
TYPE : Read - English
AUTHORS : Garofolo, John, et al.
TYPE : LDC Membership
LICENCE : LDC User Agreement
"""
import errno
import fnmatch
import os
import subprocess
impo... |
ae3d4c2abc3433346fe5c207157fc7dbe83ea9eadd42fb8e446e035767f35632 | Python | 5,551 | 168 | import json
import numpy as np
import seaborn as sns
import torch
from matplotlib import pyplot as plt
from sklearn.metrics import roc_curve, roc_auc_score, precision_recall_curve, auc
sns.set_theme()
def extract_best_model(directory, metric='val_loss'):
"""
Extract best model from a directory with checkpoin... |
5ec82ee18367a6acbe327d39df3b4e74ba428bc6de5980464e5fde9f844c06b2 | Python | 5,552 | 168 | import shutil
import os
import json
import sys
import pathlib
import copy
import hashlib
import collections
from tools.hash_value.make_hash import *
from tools.hash_value.parameters import *
def save_parameter_set(parameter_set, destination):
"""
:param parameter_set:
:param destination:
:return:
... |
66371a017252aa2e8606ba13dbc6c76307088d69159a5f46970138a9412846c5 | Python | 5,552 | 111 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from ultralytics.engine.results import Results
from ultralytics.models.yolo.detect.predict import DetectionPredictor
from ultralytics.utils import DEFAULT_CFG, ops
class SegmentationPredictor(DetectionPredictor):
... |
923aa814403653dc9ab9e21efdb61a4f0e92fe51cdf1982817937e3a01634b94 | Python | 5,552 | 143 | """Provider-specific behavior for interactive file-source template forms.
The template manager owns the generic lifecycle; capabilities own remote-service
lookups and validation that are meaningful only for one file-source type.
"""
from collections.abc import Callable
from dataclasses import (
dataclass,
fie... |
7c148dd0dcbd9d0d2429a255d2b9bfc1757e66939ee5786be60dba7cd695c0a9 | Python | 5,554 | 77 | """Протокол B2 (ЧЕРНОВИК, 13 октября 2026): конфигурация для следующей версии
эксперимента «Когда выгодно учиться». Не заморожен, прогонов по нему не было.
Что здесь уже решено (ИДЕИ_2026-10-13.md §2.5, §5.6, §5.7; REPORT_B.md §10):
* нейтральный маркерный ген marker_gene=True во всех условиях: второй
мультиплик... |
aab59e40b19f976097573eb682b533da15e4046275f1820db5fdd5e2d9af4f92 | Python | 5,554 | 139 | #!/usr/bin/env python3
"""
Dx BM — State-geometry feature sensitivity check
=================================================
Reviewer concern: 4 of the 15 features (I_A, org, I_M, I_R) are
defined in self-deposited Howie 2026a-d Zenodo preprints whose
construct validity has not been independently established. rel_alp... |
4e35016a0fbed4b29b9edf2cc086563344f69a25c3756d3c34b0e409276078b0 | Python | 5,555 | 149 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
from mmcv.cnn import build_norm_layer, ConvModule
from mmcv.runner import BaseModule
from .fpn import FPN
from ..builder import NECKS
@NECKS.register_module()
class FPNonLinearNeck(BaseModule):
"""The feature pyramid non-linear neck.
Stru... |
a722e861f4de45fb35150b4f9755b3307c6401fe73ff108df86ebdbf127878a1 | Python | 5,555 | 183 | """Tests for access-time theoretical roofline properties."""
from __future__ import annotations
import json
import pickle
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens import constants
from torchlens.quantities import Bytes
cl... |
f6355c79ba968a7c7a0c758bf96bbc9117726ae2f243264fd466a10380ca9dd7 | Python | 5,555 | 136 | import argparse
import os
import random
import time
from tqdm import tqdm
import numpy as np
import pandas as pd
import torch
from torch_geometric.data import DataLoader, DataListLoader,Batch
from torch_geometric.nn import DataParallel
from sklearn import metrics
import torch.nn.functional as F
from torch.o... |
0b82359614ed1fde57a1eb4d84e78e16cb13fdbc310ae4b3b9608d3c15c62162 | Python | 5,556 | 137 | import unittest
from numpy import ones, hstack
from cantera import Solution, one_atm
import numpy as np
from spitfire import ChemicalMechanismSpec
from os.path import join, abspath
from subprocess import getoutput
test_mech_directory = abspath(join('tests', 'test_mechanisms', 'old_xmls'))
mechs = [x.replace('.yaml', '... |
3ee1159f30e3b85adb49bf985d2fb1bf8f48cee284d8eb9dff5513b95b68677f | Python | 5,558 | 126 | import torch
import numpy as np
def pad_patient_3D(patient, shape_must_be_divisible_by=16, min_size=None):
if not (isinstance(shape_must_be_divisible_by, list) or isinstance(shape_must_be_divisible_by, tuple)):
shape_must_be_divisible_by = [shape_must_be_divisible_by] * 3
shp = patient.shape
new_s... |
94088855c5fc9e12537f717e8355def58d5cfe12d650fa7351741668eabdc69a | Python | 5,558 | 159 | import re
import numpy as np
import pandas as pd
from tqdm import tqdm
import benepar
from spacy.symbols import ORTH
import torch
from irnlm.data.utils import set_nlp_pipeline, get_ids_syntax
from irnlm.data.extract_syntactic_features import integral2syntactic
from irnlm.models.gpt2.extract_features_gpt2_integral im... |
1f2ce97b472ce5a15eaf9077fa23ad0750a30cc8280dac6251c54ce4b2d7dbfd | Python | 5,559 | 182 | # %%
import sys
sys.path.append("/home/rzhu/Documents/edamame/")
# %%
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import nptdms
from edamame import *
from edamame.analysis.InfoTheory import *
import mkl
from fig8_online_seq import *
from sklearn import preprocessing
# %%
from tqdm import ... |
1fa64df5bc9fec69765ac612573434c0e4f44dccb8c43f20726772e5bed0119b | Python | 5,561 | 223 | import math
import numpy as np
class Point(np.ndarray):
def __new__(cls, x, y=0, dtype=float):
obj = super(Point, cls).__new__(cls, shape=(2,), dtype=dtype,
buffer=None, offset=0, strides=None,
order=None)
if type(x) ... |
77138a042ed4cde3fc3d2b364e8d290f15f3d0d5f2863a4a5978d89aba34a349 | Python | 5,561 | 162 | import copy
from typing import Any
from mirp._data_import.dicom_multi_frame import ImageDicomMultiFrameStack, ImageDicomMultiFrameIndividual
from mirp._data_import.dicom_file_mr import ImageDicomFileMR
from mirp._data_import.utilities import get_pydicom_meta_tag
class ImageDicomFileMRADC(ImageDicomFileMR):
def _... |
a2cfe3c9a7fa27f96384054f747bdf059c9e1bebdeea2fbecb6804444b3995e7 | Python | 5,561 | 221 | #!/usr/bin/python3
#
# script to learn multi-output regression neural network to predict protein secondary structure
#
# (C) Yuri V. Milchevskiy, Yuri V. Kravatsky
# email: milch@eimb.ru
#
# Dependencies:
# 1. python 3 (tested with python 3.8.10)
# 2. numpy (tested with 1.22.3)
# 3. PyTorch (tested with 1.12.1)
#
##... |
c8f9f399c881f4a6f5b411893e3d7cf835698e4bb247786f770ade9079e75e76 | Python | 5,561 | 134 | """B8-18: a captured conditional must not leak an absolute source path on save.
``Trace.conditional_records`` holds ``ConditionalEvent`` objects whose
``source_file`` is the ABSOLUTE path of the user's ``forward``-defining module.
Those dataclasses had no ``PORTABLE_STATE_SPEC``, so the scrubber returned them
verbatim... |
fcf2b1c2b913a74af2e61bebf428eb628efe17c42bca7dfcbd3392ec66bc299f | Python | 5,561 | 150 | import argparse
import os
import numpy as np
import math
import torchvision.transforms as transforms
from torchvision.utils import save_image
from torch.utils.data import DataLoader
from torchvision import datasets
from torch.autograd import ... |
09479e231cbdf3869382112c261e7d8c1185819cb2963a03aaba6e5045e447e1 | Python | 5,564 | 164 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
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