sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cb14e6101c2d911a97d529e738fdc4a7444d15cefc0f4b853346a62db49f1c24 | Python | 6,064 | 206 | """Base jobs for ORCA."""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.orca import ORCA, OrcaProfile, OrcaTemplate
from quacc import get_settings
from quacc.runners.ase import Runner
from quacc.schemas.ase import Summarize
from quacc.utils.dicts import recursive_dict_merg... |
afcacf167640c05aa77dc80eefd7a79e024943177a73da7399ab1270d86ac5a1 | Python | 6,065 | 222 | #Path hack.
import sys; import os; sys.path.insert(0, os.path.abspath('..'));
import inspect
filename = inspect.getframeinfo(inspect.currentframe()).filename
path = os.path.dirname(os.path.abspath(filename))
import pickle
import numpy as np
import matplotlib.pyplot as plt
from mysql import db
class Player:
... |
d634dd075d2e99d1907268beb29be90d19dff131b58d4cefc8851753a23975ed | Python | 6,065 | 181 | '''
4SM/model.py Copyright (C) 2021 Sharif Amit Kamran, Hussein Moghnieh
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 ... |
65f9425450e0843fe2f1e90168abcd53830b7093bf9edc0abf9dc29fcdad9aa8 | Python | 6,066 | 162 | """helper module
This module contains helper functions for processing spike trains
@author Iris Yoon
irishryoon@gmail.com
"""
import numpy as np
import matplotlib.pyplot as plt
from itertools import combinations
from scipy.signal import correlate
# --------------------------------------------------------------------... |
2290f951f271c6d2022ca1058a6813e2f2d690d81c6326e9f4d6e08ca454c80e | Python | 6,067 | 194 | """"""
import logging
import warnings
import cv2
import numpy as np
from pupil_recording_interface.decorators import process
from pupil_recording_interface.process import BaseProcess
logger = logging.getLogger(__name__)
logging.captureWarnings(True)
def deprecation_warning(argument_name, process_name):
msg = (... |
9023f25b9a3937838f6866acb396acdb47900720951068c51f0b05122801222e | Python | 6,068 | 172 | import random
import unittest
import torch
import torch.nn as nn
from torch.utils.data import Dataset
from torch.utils.data.dataloader import DataLoader
from torcheeg.trainers import (ADATrainer, CenterLossTrainer, CORALTrainer,
DANNTrainer, DANTrainer, DDCTrainer, JANTrainer)
class D... |
11143c5eeabdc71cc56582ea7e6f6e744aedb0917ae0d2ea64477d4cc1665419 | Python | 6,070 | 166 | import numpy as np
import pandas as pd
from statsmodels.stats.proportion import proportion_confint
from .utils import (
_check_data_dir,
_get_filepath,
_iter_bed,
_load_chrom_mat,
_parse_cell_names,
echo,
secho,
)
def profile(data_dir, regions, output, width, strand_column, label):
""... |
146f1be1151c91ca4c106621a86bced5f3dc206f1733c29f30289169c3ee351a | Python | 6,070 | 158 | ##
# \file psf.py
# \brief Compute the Gaussian point spread function (PSF) associated with
# a slice acquisition in the coordinates of the reconstruction
# space
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date April 2016
#
# Import libraries
import numpy as np
... |
4f440570619cbad68e0b935aadccda2bfcbe3debed9ead9a48e7a30c32842786 | Python | 6,070 | 144 | from typing import Tuple
import torch
import torch.nn as nn
class InceptionConv2d(nn.Module):
def __init__(self, in_channels: int, out_channels: int, bias: bool = True):
super().__init__()
self.conv5x5 = nn.Conv2d(in_channels, out_channels, kernel_size=5, stride=1, padding=2, bias=bias)
s... |
8461005584752dbf066b6af5a93d8c425b59e92f23bde5c09e05816d241497d5 | Python | 6,071 | 177 | import argparse
import gdstk
import meep as mp
gds_file = "coupler.gds"
CELL_LAYER = 0
PORT1_LAYER = 1
PORT2_LAYER = 2
PORT3_LAYER = 3
PORT4_LAYER = 4
SOURCE_LAYER = 5
UPPER_BRANCH_LAYER = 31
LOWER_BRANCH_LAYER = 32
default_d = 0.3
t_oxide = 1.0
t_Si = 0.22
t_air = 0.78
dpml = 1
cell_thickness = dpml + t_oxide + t... |
60b3f1c2a0691a3011f8ed635570d9474e3a00ad6bd407e119929e71c60fe448 | Python | 6,072 | 165 | import time
import os
import subprocess
import sys
sys.path.insert(0, '/home/jupyter/repos/genformer')
import re
import argparse
import collections
import gzip
import math
import shutil
import matplotlib.pyplot as plt
import numpy as np
import time
from datetime import datetime
import random
import seaborn as sns
impo... |
e7dfba5322ae8a2f69520ba6cfc7f4a4870f245f9b2e3bb823ad77b1fabb06ff | Python | 6,074 | 154 | # coding=utf-8
# Copyright 2020 The Trax Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... |
84c38ce7319352357d89137b90c957fdd21f04e78c6b88093a1314753df8a790 | Python | 6,077 | 189 | from scipy.integrate import solve_ivp
import matplotlib.pyplot as plt
import numpy as np
import math as m
from mpl_toolkits.mplot3d import Axes3D
import torch
import torch.optim as optim
from Rosenbrock import Rosenbrock_func
from Quadratic import Quadratic_func
from Rastrigin import Rastrigin_func
def ... |
9dc1e7b32dc15e8200ed73f3f303025c2a664e0597ae853ca5d6458f4394e2e9 | Python | 6,077 | 120 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from lab.reports import Attribute, arithmetic_mean, geometric_mean
import common_setup
from common_setup import IssueConfig, IssueExperiment
from rel... |
a03582686cec88358cda308d3c5a7291f248c8bf3faabbd33ee585d878d24ef7 | Python | 6,077 | 183 | """Test various helper functions."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import numpy as np
import pytest
from scipy.stats import median_abs_deviation
from pyprep.utils import (
_correlate_arrays,
_eeglab_create_highpass,
_get_random_subset,
_mad,
_mat_iqr,
_mat_qu... |
f5a9dfce663a4c17d43c3c810ce758d3b92a9931e9675b4ad232fea7525670e6 | Python | 6,077 | 162 | ######################## BEGIN LICENSE BLOCK ########################
# This code was modified from latin1prober.py by Rob Speer <rob@lumino.so>.
# The Original Code is Mozilla Universal charset detector code.
#
# The Initial Developer of the Original Code is
# Netscape Communications Corporation.
# Portions created by... |
1400441684c4209bb3a6bc6b26e0484f72e59949f24463805cf78b97fa167ac4 | Python | 6,078 | 144 | from unittest import TestCase
from pyseg.diff_geom import SpaceCurve
import math
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# Test parameters
N_SAMPLES = 100
# L_BOUND = 0.5 * np.pi
# U_BOUND = 1.5 * np.pi
L_BOUND = (-0.15) * np.pi
U_BOUND = 0.5 * np.pi
C_MODE = 2
EPS = ... |
0b930af0985560660558fbf1b0e46ca99027bce5de7d8439ee6d589b496e5b93 | Python | 6,079 | 193 | # coding: utf-8
from collections import namedtuple
import datetime
import sys
import struct
PY2 = sys.version_info[0] == 2
if PY2:
int_types = (int, long)
_utc = None
else:
int_types = int
try:
_utc = datetime.timezone.utc
except AttributeError:
_utc = datetime.timezone(datetime.t... |
5dc7736303870cd5420214e9c49d68df131b1be6a9b304b53adc68029f7bb14b | Python | 6,079 | 208 | """
Cog SDK: Define machine learning models with standard Python.
This package provides the core types and classes for building Cog predictors.
Example:
from cog import BaseRunner, Input, Path
class Runner(BaseRunner):
def setup(self):
# Load model weights
self.model = load_mo... |
cf4789aaf11e79b7b4020746673d6e4a1c11ce717a7b28f3c9c042c097b14078 | Python | 6,081 | 156 | import numpy as np
import APT_interface as apt
import multiResData
import os
import pdb
import matplotlib
matplotlib.use('TkAgg')
from matplotlib import pyplot as plt
import cv2
from cvc import cvc
import pickle
def write_tfrecords(lbl_file,view,cache_dir,net,nsamples):
cache_conf = apt.create_conf(lbl_file,view,... |
5f1a313463febcc502cb348b83ae0c0e48dca4ae68656237755fa58ac4a40c3a | Python | 6,083 | 197 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
2565ae8ccc1444b0a1eb62a37c5777eac8b2c44665c17b4100470b19d54e8bdc | Python | 6,084 | 176 | """VSI format loader (Olympus/Evident slide scanner) for volume_io."""
from __future__ import annotations
import numpy as np
try:
import bioformats
import javabridge
_HAS_BIOFORMATS = True
except ImportError:
_HAS_BIOFORMATS = False
from regtools.utils.io.volume_io import (
Volum... |
608517c544713399c040e60d2fffa0ade375171a4975ccbe0d0301dfd36d1434 | Python | 6,085 | 226 | import argparse, importlib, logging, os, subprocess
from .. import __version__, __picture__
from ..logger import set_logger
def parse_args():
parser = argparse.ArgumentParser(
description="MiaoNet",
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
parser.add_argument(
"-v"... |
71ca2247b33afcfee5002a8cbdc5ed6d40d78007b9d2a5e51f56570a20fc3063 | Python | 6,086 | 118 | import os
import unittest
from hed import load_schema
from hed.errors import HedExceptions, HedFileError
class TestHedSchema(unittest.TestCase):
base_schema_dir = "../data/schema_tests/wiki_tests/"
@classmethod
def setUpClass(cls):
cls.full_base_folder = os.path.join(os.path.dirname(os.path.real... |
1b2dba7f5fe319aa7238c8043116a368e7c0a5db3741997072c6c6c255be6cb9 | Python | 6,087 | 145 | import pandas as pd
import math
import sys
# how to run this file:
# python3 molecule_padding.py n abc.txt def.txt ghi.txt
# n = amount of padding around the image
# you can enter any # of .txt files (needs to be at least 1)
cols = ['x','y','z']
file_names = sys.argv[2:]
if len(file_names) > 0:
for file_name in... |
4756b50504a9b547ed30268804a142a24af442cc77d49a0451ee1131bf15f139 | Python | 6,087 | 177 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
b224dd86fe1aa0a9aea32e7458f93fad7508417830f6ee69d19625a616f072d8 | Python | 6,087 | 173 | """Column type for a column in a ColumnMapper."""
import copy
from enum import Enum
import pandas as pd
from hed.errors.error_types import SidecarErrors
class ColumnType(Enum):
"""The overall column_type of a column in column mapper, e.g. treat it as HED tags.
Mostly internal to column mapper related code... |
d79dcb7ce2e0760cdd8bd1af91729b95d066f0a58e807dcabde0200552fb5301 | Python | 6,087 | 139 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
c1392c494a193c1876f581831801f81afe35ce9040c8fc7afadafcb6896644c2 | Python | 6,089 | 172 | """
New median implementation
"""
import numpy as np
from .buffer import Buffer
from .utils.utils import distance_buffer
class Median(Buffer):
"""New median"""
def __init__(self, L=62, dtype=float, initB=None):
Buffer.__init__(self, L=L, dtype=dtype, initB=initB)
def update(self, new_value: fl... |
1ef0c3abd6d5a9a3778dc4b70f25491cfeee4ea1736d285d91fecd152a077e4c | Python | 6,096 | 186 | """Download files with progress indicators.
"""
import email.message
import logging
import mimetypes
import os
from typing import Iterable, Optional, Tuple
from pip._vendor.requests.models import CONTENT_CHUNK_SIZE, Response
from pip._internal.cli.progress_bars import get_download_progress_renderer
from pip._internal... |
9347a3b10f6a8836141f67e18abe2592144a76428ff73fcf9ed12df7c8fdcc37 | Python | 6,096 | 193 | from __future__ import division, print_function
import unittest
import numpy as np
import matplotlib.pyplot as plt
import nitime.algorithms as ntalg
from soundsig.sound import plot_spectrogram
from soundsig.timefreq import GaussianSpectrumEstimator,MultiTaperSpectrumEstimator,timefreq,AmplitudeReassignment,PhaseR... |
2c1716d1cb027bc7a4d2deba42758e2f78f50dad1f895ec029443db540d6ecc2 | Python | 6,097 | 175 | import pytest
import os
import numpy as np
import nibabel as nib
from pathlib import Path
from pyrelimri.similarity import image_similarity
from pyrelimri.brain_icc import (voxelwise_icc, setup_atlas, roi_icc)
from nilearn.datasets import fetch_neurovault_ids
from collections import namedtuple
from nilearn.masking impo... |
a3e5e9d15b50c6374f2b83a6b069344102e31649fa6de79e74401417d603b2c9 | Python | 6,098 | 134 | import os
from typing import Dict, Iterator, List, Tuple, Union
from urllib.parse import quote, unquote
import numpy as np
import pandas as pd
from torcheeg.datasets.module.base_dataset import BaseDataset
from .base_model_selection import BaseModelSelection
from .utils import create_subset, read_indices, validate_gro... |
7268ba87adf160d5e141eeca11610c6803631c5cb9c9038fb7fd7f4425b25cc6 | Python | 6,100 | 173 | """Locations where we look for configs, install stuff, etc"""
# The following comment should be removed at some point in the future.
# mypy: strict-optional=False
# If pip's going to use distutils, it should not be using the copy that setuptools
# might have injected into the environment. This is done by removing the... |
570308446ba0e35df81365b5dd50b0179c95ea2d482423996ef0ee020c452faa | Python | 6,101 | 185 | from __future__ import annotations
from wikibaseintegrator.models.basemodel import BaseModel
from wikibaseintegrator.wbi_config import config
from wikibaseintegrator.wbi_enums import ActionIfExists
class LanguageValues(BaseModel):
def __init__(self) -> None:
self.values: dict[str, LanguageValue]... |
71b2e4c97dbbac55a853d317315235e83a5887a9a577ef7643f5957c4126405e | Python | 6,101 | 173 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.math_operations.math_operations import MathOperations
from elasticai.creator.nn.integer.quant_utils.calculate_quant_params import (
calculate_asymmetric_quant_params,
calculate_symmetric_quant_params,
)
class QParams(nn.Module):
def __i... |
b16630d97fe07f1e3580380efc3d856341c5570c725ddad4eebaa10f308b8cef | Python | 6,101 | 186 | import os
import matplotlib.pyplot as plt
from scipy.optimize import minimize
import autograd.numpy as np
from autograd import value_and_grad
rows, cols = 40, 60
# Fluid simulation code based on
# "Real-Time Fluid Dynamics for Games" by Jos Stam
# http://www.intpowertechcorp.com/GDC03.pdf
def occlude(f, occlusion... |
b6319532bdee09342c2753d835b8a9fee45251e994975da1e15bc507e3807db3 | Python | 6,101 | 154 | from jax import numpy as jnp, random, nn, jit
import numpy as np
import sys, getopt as gopt, optparse
from csdp_model import CSDP_SNN as Model
from ngclearn.utils.io_utils import makedir
## bring in ngc-learn analysis tools
from ngclearn.utils.metric_utils import measure_ACC, measure_CatNLL
from ngclearn.utils.v... |
edee85dc7020d740c2115c0b269b4b16b3bffcecb8eba85001e81d6500760f24 | Python | 6,101 | 183 | import time
import numpy as np
import pytest
from pupil_recording_interface import __version__
from pupil_recording_interface.manager import StreamManager
class TestManager:
def test_init_folder(self, tmpdir):
""""""
folder = StreamManager._init_folder(tmpdir, "here")
assert folder == tm... |
934466ce79b91672393f9058afd2983d222f8902360b7ab1d88d241f2f23501c | Python | 6,102 | 170 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..initializer import create_initializer
class BottleneckBlock(nn.Module):
expansion = 4
def __init__(self, in_channels, out_channels, stride, stage_index,
base_channels, cardinality):
super().__init__()
... |
d155325544f84752eae0e3b38fbec11370e356200c88231fd78ea79ce4685c62 | Python | 6,102 | 203 | #!/usr/bin/env python
# Written by Minh Nguyen and CBIG under MIT license:
# https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
from __future__ import print_function, division
import argparse
import json
import time
import pickle
import numpy as np
import torch
import cbig.Nguyen2020.misc as misc
from cbig.N... |
b6baad9dbae3f25a230c0048eb3490defe27fc14e52d16d548185a08a3dba7ec | Python | 6,104 | 108 | import torch
from torch import nn
from torch_cluster import knn_graph, radius_graph
from torchdrug import core, data
from torchdrug.layers import functional
from torchdrug.core import Registry as R
from torch_scatter import scatter_min
# ** should be registered in torchdrug.layers.geometry.__init__, for to b... |
b7d7846e737edbefdde760130635c231746eca5a5fe995142cf04717d4f27749 | Python | 6,105 | 195 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
35cbe46ba592c42e00b0dc220cef732d5dd2fcce670aaedc1c06da314c1bce1b | Python | 6,108 | 154 | # -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
rec_header_dtd = \
[
("nx", "i4"), # Number of columns
("ny", "i4"), # Number of rows
("nz", "i4"), # Number of sections
("mode", "i4"), # Types of pixels in the image. Values used by IMOD:
... |
b5c0d51c6520c76580f0585f25601c9aa909afa050310a977590761e39d151d1 | Python | 6,108 | 147 | import matplotlib
matplotlib.rcParams['figure.facecolor'] = '1.'
matplotlib.use('Agg')
import ants
import time
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from skimage.filters import threshold_otsu
from nibabel.processing import resample_to_output, ... |
29c5c89318753201fe55d161cc1005d5e31eb7c37ad8992d04b948bc1f8bf99e | Python | 6,109 | 153 | """Single-image RegistrationTab: Cancel terminates the run + Open Output Folder.
Built under offscreen Qt. Verifies that:
* the Cancel button is wired to a handler that calls the terminal-job mixin's
``cancel_job()`` - i.e. it really stops the running registration process,
not merely resets the UI;
* an "Ope... |
46642c5bcf9af56ef028636065a9919d2bfee8e5311a195f2ed320f29409d105 | Python | 6,109 | 99 | # -*- coding: utf-8 -*-
"""
Extract Volume statistics from recon-all segmentations
"""
import os
import glob
import subprocess
from nipype import logging
from nipype.interfaces.base import (
traits,
TraitedSpec,
Directory,
BaseInterfaceInputSpec,
BaseInterface
)
from traits.trait_types import Str
_... |
56dec808869e1a378f282dfe4def9f7ebdb03652109aeb89aa2f859e45debb43 | Python | 6,109 | 175 | import sys, os
import numpy as np
import keras
from keras.models import Model
from keras.layers import Input, Dense, Dropout, Flatten
from keras.layers.merge import concatenate
from keras.layers.convolutional import Conv2D, Conv1D
from keras.layers.pooling import MaxPooling2D, AveragePooling1D
from keras import backend... |
22272d1798430facf9a869466a8032ce87f2804aefe8c3ebe906e93dd5bf78f4 | Python | 6,110 | 145 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
from qtpy import QtGui, QtCore, QtWidgets
from qtpy.QtWidgets import QMainWindow, QApplication, QDialog, QWidget, QScrollBar, QSlider, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar,... |
314ec1d54b48b88a97e506214bfe8edabdbafb5d617ba3804002d5d1e4f42073 | Python | 6,111 | 103 | #! /usr/bin/env python3
import os
import subprocess
import logging
import APT_interface
class cd :
"""Context manager for changing the current working directory, and automagically changing back when done"""
def __init__(self, path):
self.path = path
def __enter__(self):
self.old_path = ... |
5328db4c6c35fef92568d32c8a6b10779e2c1e73af9f18341d2db51ab1dac9af | Python | 6,111 | 153 | """
Unit tests for regtools/ome_zarr_converter/points.py
The `load_points` entry point now delegates to
`regtools.utils.io.points_io.load_points_file`, whose format-detection,
TXT, and CSV behaviors are covered in test_points_io.py. These tests
focus on what `ome_zarr_converter.points` owns: the Neuroglancer pr... |
6a91a72bbd4ffebdfc7348c5b955cf4586893a5feb8a327ea5b967f6997c1166 | Python | 6,111 | 179 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
f732493a407e2c1b78f37959016cdd2e13070343786ec285fcbeb56444f1935c | Python | 6,111 | 125 | import os
from typing import Tuple, Callable, Union
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
from ..utils import get_random_dir_path
from .utils import create_subset, ensure_cache, read_indices, write_indices
def train_test_split_cross_sub... |
1096677f61f2a19e3736bbe170fc3379b9f1695c77a37a0143f28929f6d43436 | Python | 6,112 | 146 | import pandas as pd
import numpy as np
from tests.mock_data import MockCvOutput, MockCuppaClassifier, MockTrainingData
from cuppa.classifier.cuppa_prediction import CuppaPredictionBuilder, CuppaPrediction, CuppaPredSummaryBuilder, CuppaPredSummary
class TestCuppaPredictionBuilder:
def test_can_build_predictions... |
a8bab903bb7aeec5297dde11612e187b766b7f6c821b122201975a15c146c46a | Python | 6,113 | 134 | import os
import re
from typing import Iterator, Dict, Tuple, Union
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
from .base_model_selection import BaseModelSelection
from .utils import create_subset, read_indices, write_indices
class KFoldCross... |
89c5b1a013c84c7179e1a2d75c34605ff0469afb97c19b2a22182a26bef6e4e8 | Python | 6,115 | 181 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
e9405133b3ba6e75063de46506ca0a71b873869b0b78f7569ee45bab0f1a1470 | Python | 6,116 | 167 | """
Unit tests for regtools/utils/image_processing.py
Covers:
- auto_contrast
- preprocess
- remove_artifacts
"""
import numpy as np
import cv2
import pytest
# ===========================================================================
# auto_contrast
# ========================================... |
1eaebc70087d526664ff89882fa052a4f2b7327e7c80ac3302aae8fa88131e0f | Python | 6,117 | 132 | from importlib.util import find_spec
import anndata as ad
import numpy as np
import pandas as pd
import pytest
import statsmodels.api as sm
if find_spec("formulaic_contrasts") is None or find_spec("formulaic") is None:
pytestmark = pytest.mark.skip(reason="formulaic_contrasts and formulaic not available")
def _... |
9b24700e5fe4beaf35838041fbddc68c6fa1dd9b1aab7cb52f5e45701c747b94 | Python | 6,117 | 146 | #!/usr/bin/env python
"""
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Fr... |
55a5ca2079b94e4f9d8f3ad08d3f7fb6e3a4350012226ae403ed9495ed0cf8a5 | Python | 6,118 | 157 | import csv
import os
import fnmatch
import numpy as np
from mahotas.features.texture import haralick_labels
import nibabel as nib
import ExtendGaborFeatures
import Biopsy5by5WindowV3
import FirstOrderFeatures
import MultiModality
def String_f(listOfStrings,Pstrings):
for Strings in listOfStrings:
... |
572695723a473a535e9848dfc93dce0eeb3bbab7727b92b9229444b65e76ab54 | Python | 6,118 | 160 |
import argparse
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
import random
from dataloaders.data_loader_s2r import S2R_Dataset_train, S2R_Dataset_test
from torch.utils.data import DataLoader
from model.resinf_foreal import ResInf
from engine_s2r import *
import wandb
from utils imp... |
b5a9876b017320b15902b252f5502eca5a0349a554bace5f8553e0c1e56c6d7d | Python | 6,118 | 146 | from neuron import h
from network.Segment import Segment
import numpy as np
class Cell(object):
def __init__(self, index: int, name: str, cell_param: dict) -> None:
# name: cell name, string
# index: cell index, int
# cell_param: cell parameters, dictionary
self.index = index ... |
1faa713fc7d20072b5eb358e622b43f054164e8ea6ae461a2ad053ae3a0aadb1 | Python | 6,120 | 194 | import json
from collections import Counter
import warnings
from tqdm.auto import tqdm
import random
import math
import numpy as np
import pandas as pd
# from pandas.core.common import SettingWithCopyWarning
# warnings.simplefilter(action="ignore", category=SettingWithCopyWarning)
pd.set_option('mode.chained_assignme... |
4bec8a40696f218922c2545728803a817449ad24fe0517de834b0ffec87c6028 | Python | 6,120 | 132 | import os
from typing import Tuple, Union
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
from ..utils import get_random_dir_path
from .utils import create_subset, ensure_cache, read_indices, write_indices
def train_test_split_cross_trial(
... |
0311f5857f3d2d1d41d9f9115a487a050ebaa6821e7ee831b44efcee184bb0ea | Python | 6,121 | 163 | from __future__ import annotations
from collections import defaultdict
import pandas as pd
from joblib import Parallel, delayed
from loguru import logger
from pandas._typing import FilePath
from tqdm import tqdm
from tqdm_joblib import tqdm_joblib
from .pair_evaluator import PairEvaluator, DeltaType
def get_pair_e... |
09f9d2c3037074127459a16910c82180e62d26c189d357853f2de535167d967e | Python | 6,121 | 202 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
d835fd80a9654ae4b28a00ece3e0ba8de6ecd242daf48c0222a3a6e0eae5d286 | Python | 6,122 | 186 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import os
import time
import random
import argparse
import numpy as np
from pathlib import PurePath
import keras
from keras import backend as K
from keras.o... |
e92992c7771aee861c1d8f642923e3c646671456efb80f473211366d496631fc | Python | 6,122 | 153 | """Multi-slice propagation of a contour edit.
Given a SliceEditState on slice Z, propagate the same per-handle
displacement to neighbouring slices Z±N. The naive copy fails
because the neighbour slice's pristine contour has a different
shape - same anatomical region, slightly different boundary at
that z. The ri... |
abfd28c7ef2a5dd527a07fbcde59ee2203a6bd3843820ec2d9d1253ad841768f | Python | 6,124 | 84 | """This file is to explore how the hyperparameters influence neural network dynamics"""
import os.path as path
import datetime
import argparse
from eworm.network import process
chemotaxis_neuron = ["AWAL", "AWAR", "AWCL", "AWCR"]
# 82
sensory_neuron = ["ASIL", "ASIR", "ASJL", "ASJR", "AWAL", "AWAR", "ASGL", "ASGR", ... |
68e3b0b46c9cc3a2e7156129ea5d3a396364dec1f03931a026b6a171a5077897 | Python | 6,125 | 240 | from __future__ import annotations
import re
from pathlib import Path
from typing import TYPE_CHECKING
from ase.calculators.genericfileio import (
BaseProfile,
CalculatorTemplate,
GenericFileIOCalculator,
read_stdout,
)
from quacc.calculators.mrcc.io import read_mrcc_outputs, write_mrcc
if TYPE_CHEC... |
6dc2a263edc774df61df4c66fb1773981d116af79f60845a02247eddb0a8d862 | Python | 6,125 | 182 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
3ea64fb4dc94995830e4cd67a47db81615909802ce98126da771143474a8dc72 | Python | 6,126 | 172 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
56b71e36210fe8bbb9c1ecf9646f3ec626ba6e0573a54a8b1b24c3e7fa64d71c | Python | 6,128 | 131 | from typing import List
import torch
import torch.nn as nn
from .mmd_like import _MMDLikeTrainer
def _compute_covariance(data, eps: float = 1e-6):
n = data.size(0)
device = data.device
ones_vector = torch.ones(n).resize(1, n).to(device=device)
one_onto_D = torch.mm(ones_vector, data)
mult_rig... |
f7091cb698f1656e1dfd8681b6d6183cc7ee68416f07ea803f9874cb62e96a05 | Python | 6,128 | 176 | # -*- coding: utf-8 -*-
"""
Created on 15 october 2023
@author: divyoj
"""
## importing libraries:
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import os
# # note that this must be executed before 'import numba'
# os.environ... |
53cce7c4fbbe20fe459c91d470704adbb0ec90bbc6fa079610708eb7198b691c | Python | 6,129 | 153 | #! /usr/bin/env python
from __future__ import print_function
from collections import deque, defaultdict
import itertools
import time
import invariants
import options
import pddl
import timers
class BalanceChecker(object):
def __init__(self, task, reachable_action_params):
self.predicates_to_add_actions ... |
6225d0cdbefa83e87c8e470ea6a8f7343a2059d366ae75e65be6ce0cb3570c62 | Python | 6,129 | 139 | import numpy as np
import os
import pandas as pd
import torch
import torchvision
from constants import *
from src.utils import map_to_score_grid, score_to_class
from src.dataloaders.rocf_dataloader import get_dataloader
from config_eval import config as cfg_eval
class RegressionEvaluator:
def __init__(self, mod... |
341a69256e79f44c6b480dd079a648efb48655c2917ba09ac198adc08c1c0562 | Python | 6,130 | 137 | from typing import List, Tuple, Union
import numpy as np
import torch
from torch import nn
from torch.utils.data import DataLoader
from ..classifier import ClassifierTrainer
class WCELossTrainer(ClassifierTrainer):
r'''
A trainer class for EEG classification with Weighted Cross Entropy (WCE) loss for imb... |
15a27472f35f712d11871ff6cdca7d3dea7996f40fc3c03d0501dbcf7775f21d | Python | 6,131 | 188 | """High-pass filter and locally detrend the EEG signal."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import logging
import mne
import numpy as np
from pyprep.utils import _eeglab_create_highpass, _eeglab_fir_filter
logger = logging.getLogger(__name__)
def removeTrend(
EEG,
sample_ra... |
93cb2aa1bcd187c183ec92ba388379e06c7735d84d4d316a7aa380ff5c035045 | Python | 6,131 | 176 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
52471e1140fd165767a9065ea96a8b5dd19b30b5f0f858b93c9c34e70da90101 | Python | 6,132 | 143 | ## Importing these packages is specific for this simulation case
import numpy as np
import hmp
from hmp import simulations
from hmp.models import EventModel
from hmp.patterns import HalfSine
from hmp.distributions import Gamma
from hmp.patterndata import PatternData
from test_io import init_data, init_data_large, i... |
13bc8265557fe970e4abbb5b2c79987760802328fb5507297fbad08475cc323f | Python | 6,133 | 179 | from __future__ import annotations
# built-in
from collections import defaultdict
from itertools import groupby, zip_longest
from typing import Any, Iterator, Sequence, TypeVar
# app
from .base import Base as _Base, BaseSimilarity as _BaseSimilarity
try:
# external
import numpy
except ImportError:
numpy... |
13d95e5e00fb0ddd4a94e50290c63c9b4aba4158107d522191cedaf7521e0d16 | Python | 6,133 | 236 | from glob2 import glob
import tifffile
import os
import numpy as np
import matplotlib.pyplot as plt
from skimage import exposure
from imgaug import augmenters as iaa
import cv2
import tensorflow as tf
from tensorflow.keras.preprocessing import image
def normalize99(X):
"""normalize image so 0.0 is 0.01st percentil... |
47639b6d9f3fdfe46a728a3e3ea081f017f75b5d1d5fc6f37ce8b5a31d88d80a | Python | 6,133 | 135 | from datetime import datetime
import gzip
import json
import pandas as pd
#Defining JSON data loading function
def json_loading(f,g,s,fold):
begin_time = datetime.now()
genes_df = pd.read_csv(g, sep='\t')
genes_list = genes_df['gene symbol'].tolist()
#Creating a list containing the ... |
27244af281531d204ccfce92e5f1a79f972022630ef83290a2361840099c3cc2 | Python | 6,134 | 180 | import os
import argparse
basepairs = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N',
'W': 'W', 'S': 'S', 'M': 'K', 'K': 'M', 'R': 'Y',
'Y': 'R', 'B': 'V', 'V': 'B', 'D': 'H', 'H': "D",
'Z': 'Z'}
iupac_alphabets = {'A': ['A'], 'T': ['T'], 'C': ['C'], 'G': ['G'],
... |
2b44dc62dbf8aa9ddac4446942080d3d6c1c4d8a60845e6814f4b0af9877f6dc | Python | 6,138 | 120 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from lab.reports import Attribute, arithmetic_mean, geometric_mean
import common_setup
from common_setup import IssueConfig, IssueExperiment
from rel... |
1de58aecc08bf8a7eb899378b13787e725fa36a783d1c88681c1318c1685cd85 | Python | 6,140 | 179 | # test_levenshtein.py
import pytest
from fba.levenshtein import (
indexkeys,
bytes2set,
set2bytes,
create_index,
query_index,
select_query,
format_one_query,
match_barcodes_paired_fastss
)
test_data = [
('ACGT', 0, {'ACGT'}),
('ACGT', 1, {'ACG', 'ACGT', 'ACT', 'AGT', 'CGT'}),
... |
a591db5877a6bc05583a262d448f9f4079d2ee25eded3406efcea2fdb3fd591a | Python | 6,140 | 141 | from __future__ import print_function
from collections import namedtuple
from pddlstream.algorithms.constraints import to_constant, ORDER_PREDICATE, ASSIGNED_PREDICATE, \
get_internal_prefix
from pddlstream.algorithms.downward import make_action, make_domain, make_predicate
from pddlstream.algorithms.focused impo... |
1d721f4ee5b7cd1074b03936a505200feb83a1b34dde916a9a63be386f977251 | Python | 6,141 | 157 | import os
from csv import DictReader
from glob import glob
from datetime import datetime
import scipy.sparse as sp_sparse
from .utils import _check_data_dir, _get_filepath, _load_chrom_mat, echo, secho
def _filter_by_name(file, cell_stats_path, keep=True):
fpath = _get_filepath(file)
cells_to_keep_idx = []
... |
10af0e022496ece4fc8f69023e7b4ffc86c968656039c69377fe59f5bd7fc882 | Python | 6,142 | 167 | import itertools
import numpy as np
import pandas as pd
import scipy.stats
def _power(X, power):
return X**power if isinstance(X, np.ndarray) else X.power(power)
def asarray(x):
return x.toarray() if scipy.sparse.issparse(x) else x
class DE:
def __init__(
self,
series: pd.Series,
... |
14b5d3573bc4a3295be6915137cb9b9579365bef7811661ccd2d6d96d3b3256c | Python | 6,143 | 162 | # Node group "Symmetry Instance" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are regene... |
3c18bf59e8294c8beb0c5ef0eeddf42460c26af6d60be02276441b46e938c2a5 | Python | 6,143 | 169 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
4493bbf85c072bbdcff549d517680d801cf38816f0f8f7e6442224e3a0e761e2 | Python | 6,143 | 182 | import json
from pathlib import Path
import numpy as np
import torch
import tqdm
from scipy.stats import pearsonr, spearmanr
from .prix_fixe_net import PrixFixeNet
from .dataprocessor import DataProcessor
from typing import Any
from abc import ABCMeta, abstractmethod
# default metrics to compute
DEFAULT_METRICS = ... |
5d5f35aa01231172109eb184fc5dfce35dc1ce31d7bd68b6ac1d242f71d9debd | Python | 6,143 | 134 | import os
from pathlib import Path
import subprocess
import sys
import textwrap
import unittest
class TestOptionalModelDependencies(unittest.TestCase):
def run_without(self, modules, body):
root = Path(__file__).resolve().parents[2]
script = '''
import importlib.abc
import sys
import torch
import ... |
601525e53addd1d21f7022a095babdefb5d4c1d90a11a9c6b1e934e7e7271568 | Python | 6,143 | 139 | #!/usr/bin/env python
import os
import argparse
import sys
sys.path.append(os.path.dirname(__file__)+'/..')
from maggie import score, utils, visual
import numpy as np
import pandas as pd
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='MAGGIE framework working with FASTA files')
pars... |
909cc0378b4c1f28e33a65594db9bbbf1921c44ac44c1feb828c88b34e2f0d5b | Python | 6,143 | 141 | """Define observation extractor class."""
import re
import itertools
from collections import defaultdict
from tqdm import tqdm
from constants import *
import bioc
class Extractor(object):
"""Extract observations from impression sections of reports."""
def __init__(self, mention_phrases_dir, unmention_phrases... |
c119ae56d02d8a1baf0b0581a89e861501a1285a7115b2bd4e2a21cb13a8f863 | Python | 6,143 | 166 | # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/00_ode.ipynb.
# %% auto 0
__all__ = ['ode_solve', 'ODEF', 'ODEAdjoint', 'NeuralODE']
# %% ../nbs/00_ode.ipynb 3
import os, math, numpy as np
import torch
import torch.nn as nn
def ode_solve(z0, t0, t1, f):
"""
Simplest Euler ODE initial value solver
"""
... |
dcd7cc35a7135f5e2f03e08065dc8675ab2dbe39d26b292529b18336bc4cc950 | Python | 6,143 | 152 | # Node-group asset "Evaluate While Planar" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_... |
1768265734df9a0fe45533ede873f53566bbeb21b106fcd93f16fcc2ed7b725f | Python | 6,144 | 197 | import torch
from torch import nn
from torch_scatter import scatter_mean, scatter_add, scatter_max, scatter_softmax
class Readout(nn.Module):
def __init__(self, type="node"):
super(Readout, self).__init__()
self.type = type
def get_index2graph(self, graph):
if self.type == "node":
... |
2481d68c1c83970aab129f70d52258264aeb4a492afe7312d791202c8055419b | Python | 6,145 | 162 | import unittest
from hed.errors import ErrorHandler
from hed.models import HedString
from hed.schema import load_schema_version
class TestBaseTagBase(unittest.TestCase):
schema_version = "8.0.0"
@classmethod
def setUpClass(cls):
cls.hed_schema = load_schema_version(cls.schema_version)
cl... |
fde441d219fa806f58fd086b4f76b4e75659307d8d7ff747d67a00551044d2c4 | Python | 6,145 | 174 | from functools import partial
import torch
import torch.nn as nn
from torch.nn import Parameter
import torch.nn.functional as F
class Flatten(nn.Module):
def forward(self, x):
return x.view(x.size(0), -1)
class SELayer(nn.Module):
def __init__(self, channel, reduction=16, ret_att=False):
sup... |
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