sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8e92efc3dc73eeac37111c6ba1c19d040e462c843f88da5606df88aed12238de | Python | 2,621 | 83 | """A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
from setuptools import setup, find_packages
from os import path
from io import open as io_open
TEST_REQUIRES = [
# testing and coverage
'pyte... |
da57f7e861c170cd5f51dd227b3e3d115b087db78908dcf4bfa80660bb463eba | Python | 2,621 | 73 | #!/usr/bin/python
#
## @file
#
# For running modules outside of HAL.
#
# Hazen 03/14
#
# Add current storm-control directory to sys.path
import imp
imp.load_source("setPath", "../sc_library/setPath.py")
import importlib
import sys
from PyQt5 import QtWidgets
import storm_control.sc_library.parameters as params
def ... |
e5f7f55d2eac381a72f9ebe0846a8e27ad7b6f91dfd663b55cc16a00693c5fff | Python | 2,621 | 73 | ################## PURPOSE #################
# This script removes duplicated coordinates that resulted from Bedtools merging
# and removes NULLs if they are not stand-alone values in a cell
################# ASSUMPTION ###############
############################################
# Imports in the pep8 order https:/... |
f1d98ac2ab1eeab3712f90fe0f8e9bf6db6aa828d7c2f2eeef4fc3a244e584d0 | Python | 2,621 | 79 | from qtpy.QtCore import Qt
from qtpy.QtWidgets import (
QApplication,
QDialog,
QHBoxLayout,
QLabel,
QMessageBox,
QPushButton,
QSizePolicy,
QSpacerItem,
QStyle,
QTextEdit,
QVBoxLayout,
)
class WarningDialog(QDialog):
def __init__(self, text: str, title: str = "Warnings",... |
5c3e352ba0ee400bc0fde64dd886a786c50f7015462354bfa9954b9e628ad390 | Python | 2,622 | 73 | # # load the necessary modules
# from dmipy.core import modeling_framework
# from dmipy.core.acquisition_scheme import acquisition_scheme_from_bvalues
# from os.path import join
# import numpy as np
# from dmipy.signal_models import cylinder_models
# # the HCP acquisition parameters are saved in the following toolbox ... |
8c7f8bc33ad0755da1a24d247b2b363242110c4f142d56024e012e5ae04a7cc2 | Python | 2,622 | 49 | import torch
from torch import nn
from .local_channel_attention import LocalChannelAttention
from .global_channel_attention import GlobalChannelAttention
from .local_spatial_attention import LocalSpatialAttention
from .global_spatial_attention import GlobalSpatialAttention
class GLAM(nn.Module):
def __init__... |
b46e0b0d6dec141c630c8cdac520a2829d9ff102c572d2136fdf8ceca64c3389 | Python | 2,622 | 82 | import logging
from ..config import ObservableCollection
from ..qt import *
from .. import thalamus_pb2
from ..task_controller.util import create_task_with_exc_handling
LOGGER = logging.getLogger(__name__)
class LuaWidget(QWidget):
def __init__(self, config, stub):
super().__init__()
if "Equations" not in... |
ccffc59467cac412e8b7af6ad86e8353ffff589ce004b6fa9fa086da5964b2e1 | Python | 2,622 | 83 | ################## PURPOSE #################
# This script removes duplicated coordinates that resulted from Bedtools merging
# and removes NULLs if they are not stand-alone values in a cell
################# ASSUMPTION ###############
############################################
# Imports in the pep8 order https:/... |
e4fff149fd9d9975cb9baa86f3276e65247299ca81b0deda4476927fba4efd67 | Python | 2,623 | 72 | import os
import os.path as osp
import torch
import numpy as np
import scipy
import pandas as pd
import argparse
import os
import torch_geometric.transforms as T
from torch_geometric.utils import to_networkx
from torch_geometric.data import Data
parser = argparse.ArgumentParser(description='display graph features and ... |
fcefe68be5bf0a5943195f3a8ad6b9f934c8bba94f163003950456b31c7bfb3e | Python | 2,623 | 69 | # @SNTService snt
# @UIService ui
"""
file: Scripted_Tracing_Demo.py
author: Tiago Ferreira, Cameron Arshadi
version: 20260731
info: Exemplifies how to programmatically perform A* tracing between two
points without GUI interaction, which allows for automated tracing
of relatively simple struct... |
01e4c31ed69a0baf2b0e323a36c2260e6deecded2e0ba54c6740b89d666b4153 | Python | 2,624 | 82 | #!/usr/bin/env python3
# Copyright (C) 2025 Paolo Vincenzo Fioretti, Michela Roccuzzo, Enrico Saccon,
# Maria Pennuto, Manuela Basso
# 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 vers... |
1b81c93f9646eeb71fc93a3cd0fcb9b91affe0fe2ede3a44e488e8ef7329f4d8 | Python | 2,624 | 66 | #!/usr/bin/env python3
"""Record a synthetic grayscale video stream into a Thalamus capture file.
Thalamus stores camera data as ``image`` records. Each record carries the raw
frame bytes plus its width, height, pixel format, and frame interval. This
example writes a short ``Gray`` (8-bit) clip of a vertical bar swe... |
2f1584c2fc8c0a2f9f2553e49e6b24e0735c94b8a7ab4538d13f429b3301456d | Python | 2,624 | 63 | import functools
from torchvision.models import densenet121
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.check_submission import check_models
def get_model(name... |
af5ddd6610b969d01b3ff5f18df5c105ff32563dab1c4921782e30fecfbb38ec | Python | 2,624 | 78 | """Functions to handle task data."""
import numpy as np
def epoch(
data: np.ndarray, time_index: np.ndarray, pre: int, post: int, pad: bool = False
) -> np.ndarray:
"""Transform (time, channels) data to (epochs, time, channels) data.
Given a series of triggers given by :code:`time_index`, spit a continu... |
fc6f3f955d971a8a602eb928282ebdf596d344decb3bc040f835ee0dddaeda21 | Python | 2,624 | 63 | import functools
from torchvision.models import densenet169
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.check_submission import check_models
def get_model(name... |
1596a6d07f4d50b52ae58f333c0eed99892c0b5e3e09d206516a16a2e9674d6c | Python | 2,625 | 63 | import argparse
import os
import pandas as pd
from tqdm import tqdm
from utils.utils import load_coords
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='make single mutant tsv')
parser.add_argument("-d", "--dataset", type=str, default=None)
parser.add_argument("--pdb_file", type=st... |
c13d365bd36e999c0d18f435680acc44390638a83c56023e03c6f3cd7262d45d | Python | 2,625 | 56 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'infoBox.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_infoBox(object):
def setupUi(self, infoBox):
infoBox.setObje... |
4099d712d1b9544a0641ceba16dfdeb01129307953a4e39b4fd914d95d077a9e | Python | 2,626 | 82 | # -*- coding: UTF-8 -*-
# Copyright (c) 2019 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
#
... |
aba3d567d87f92b031bd4cc320a45d38a5b180c855bbe3b4102d42d0d025bf81 | Python | 2,626 | 68 | import traits
from nipype.interfaces import utility
from PUMI.engine import FuncPipeline, NestedNode as Node
@FuncPipeline(inputspec_fields=['ts_files', 'fd_files', 'scrub_threshold'],
outputspec_fields=['features', 'out_file'])
def calculate_connectivity(wf, **kwargs):
def calc_connectivity(ts_fil... |
5e1f75d4f3ce0500c852d20c1328fccc668305f7c3f8d9f6ee1bb67c6eb00b67 | Python | 2,627 | 78 | import pandas as pd
from abc import ABC, abstractmethod
class SurvivalBase(ABC):
"""
Interface class for causal survival analysis with fixed baseline covariates.
"""
@abstractmethod
def fit(self,
X: pd.DataFrame,
a: pd.Series,
t: pd.Series,
y: pd.Ser... |
9e4306ccb1965f15c9d7258f611247ab7b634d50dfc2950bc1e4813bfa18b594 | Python | 2,627 | 81 | import os
import json
from nipype.interfaces.base import (
CommandLineInputSpec,
TraitedSpec,
CommandLine,
)
from traits.api import Str, Int, Bool
class SynthSRInputSpec(CommandLineInputSpec):
input = Str(mandatory=True, argstr="--i %s", position=0, desc="Image(s) to super-resolve.")
output = Str(... |
0571bec9c72b0b6f7405a5683c9ef013990be4134f11d02bd2080c35224081a9 | Python | 2,628 | 87 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import logging
from contextlib import contextmanager
from functools import wraps
import torch
__all__ = ["retry_if_cuda_oom"]
@contextmanager
def _ignore_torch_cuda_oom():
"""
A context which ignores CUDA OOM exception from pytorch.
... |
11fc7df56af279935a631b7ae98e1e936239f00e1ca332af93165bb08bb102dd | Python | 2,629 | 76 | from .base import WaveformBenchmarkDataset
class LFEStacksCascadiaBostock2015(WaveformBenchmarkDataset):
"""
Low-frequency earthquake stacks underneath Vancouver Island, Cascadia, Canada/USA based on the catalog by
Bostock et al (2015). Compiled to SeisBench format by Münchmeyer et al (2024).
"""
... |
2db69625801c005b1cae38008b134da613fd922036b3e3afb791267f74684917 | Python | 2,629 | 87 | #!/usr/bin/env python3
import vtk
import vtk.util.numpy_support as VN
import numpy
import argparse
from pathlib import Path
#command line interface
parser = argparse.ArgumentParser()
parser.add_argument('file0')
parser.add_argument('file1')
parser.add_argument('output', nargs='?')
args = parser.parse_args()
if not Pa... |
30118ac6ea8f40940b3407159c5f5145ee75f665a412546e92166742e4f66198 | Python | 2,629 | 70 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
import numpy as np
import torch
from ultralytics.utils import LOGGER
from .base import BaseBackend
class DeepXBackend(BaseBackend):
"""DEEPX NPU inference backend for DEEPX hardware... |
3cec1aaf4e90a7cff1e1b5e1ba8e004f0e031d3a5761bfc3ff8a2ae52bf93d7f | Python | 2,629 | 53 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'adjust_contrast_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.7
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dial... |
591092838467ad1189081cd0e304f5b752e0d2d6232f1915ef0034d966003b17 | Python | 2,629 | 81 | #!/usr/bin/python
#
## @file
#
# Test communiction with Nikon TI microscope.
#
# Hazen 04/14
#
import MMCorePy
import time
mmc1 = MMCorePy.CMMCore()
mmc1.loadDevice('TIScope', 'NikonTI', 'TIScope')
mmc1.loadDevice('TITIRF', 'NikonTI', 'TITIRF')
mmc1.loadDevice('TIFilterBlock1', 'NikonTI', 'TIFilterBlock1')
mmc1.initi... |
71b477d5e0c2bbc78fc090e9e76c33eac7ea8e39ec15b8b6d568a8fd8ab9b777 | Python | 2,629 | 100 | from pathlib import Path
import subprocess
import sys
from typing import ClassVar, Optional
from argclz import argument, int_tuple_type
from neuralib.rastermap import RasterMapResult
from neuralib.util.verbose import fprint
from .cli_core import CommonOptions
__all__ = ['RasterMapOptions']
class RasterMapOptions(C... |
9e7ba5dd5058c7c30fbd1f70d217e8cfbfba5aa788aa8a48b833c9b53a22169f | Python | 2,629 | 87 | from typing import Any
import pandas as pd
from gamma.utils import association as gamma_association
from .base import AbstractAssociator
class GammaAssociator(AbstractAssociator):
def __init__(self, config: dict[str, Any], **kwargs) -> None:
super().__init__(**kwargs)
self.config = self._adjust... |
cb6e7fd1d2bc9a0386386138102900cdf93121c1697e24069a46591692e7401e | Python | 2,629 | 75 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import math
import numpy as np
allShapes = {
"square" : [[1.2602,0],[0,1.2602], [1.2602,1.2602],[0.6301,0.6301]], # noqa
"rectangle" : [[1.5,0], [0,1], [1.5,1], [0.75,0.5]], # noqa
"isoTrapezoid" : [[0.7445,0],[-0.3648,... |
6db22707bdc0f18012596d91e631882de6e29d54e8a77f7ec2610a28a72b97a7 | Python | 2,632 | 80 | from skeleton_keys.cmds.depth_profiles_from_aligned_swcs import (
ProfilesFromAlignedSwcsParameters,
main as depth_profile_main,
)
from skeleton_keys.cmds.process_morphology_features import (
ProcessMorphologyFeaturesParameters,
main as morph_feat_main,
)
import argschema
from taskqueue import queueab... |
9883e18072851730d668602348f3198ff16986549910d1e52f94fa1b9848b63f | Python | 2,632 | 83 | import pytest
from eir.setup.config_validation import validate_no_duplicate_columns
def test_validate_no_duplicate_columns_no_duplicates():
columns = ["col1", "col2", "col3"]
validate_no_duplicate_columns(
columns=columns,
config_type="Tabular input",
config_name="test_input",
)
... |
9a73ee17f7b0d35252bbd451c58e549e5499d786ede483cb501203c2c6ac3ff0 | Python | 2,632 | 89 | import pandas as pd
import numpy as np
import json
from stg_PopPK.main_utils import run_train
import argparse
import os
from pathlib import Path
ROOT_PATH = Path(__file__).resolve().parent.parent
DATA_PATH = ROOT_PATH / "data"
def read_data(scenario):
csv_data_train = pd.read_csv(DATA_PATH / scenario / "train.cs... |
dac465fe86466be400063765d186559c6cfd7c56204895d5b71f627190c69e63 | Python | 2,633 | 67 | import functools
import torch
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.check_submission import check_models
def get_model(name):
"""
This method fet... |
430258c025fbb0d8b2aa3bc1fa9d09e5635fea6338b7c46a90ba75e2c76c54d4 | Python | 2,634 | 61 | import os
from scipy.io import loadmat, savemat
"""
Usage: good_listen_subjects, good_motor_subjects,good_error_subjects,musicians,nonmusicians = load_subject_lists_LME()
"""
all_subjects = ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21']
... |
540e72468df62156a467fe6763be4a02b7da5e765b00dcd39313151839be728e | Python | 2,634 | 58 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import torch
from ultralytics.engine.results import Results
from ultralytics.models.yolo.detect.predict import DetectionPredictor
from ultralytics.utils import DEFAULT_CFG, ops
class OBBPredictor(DetectionPredict... |
6f403206cb62ba285b3608f90c570bde5f94204dbbd266c266e593724fe39288 | Python | 2,634 | 89 | from typing import Type
import numpy as np
from neuron import h
from ..cells.neuron_cell import NeuronCell
from .simulation import WaveformType
from .spike_simulation import SpikeSimulation
from neuron.units import ms, mV
class ThresholdFactorSimulation(SpikeSimulation):
"""A NEURON simulation with the function... |
8b625a70ee3761a52a313c59a5e7c0f70a5a2bd7241feb284b31b9b3d387eec6 | Python | 2,634 | 101 | # coding=utf-8
"""
Module to download additional data and resources that
are not included in releases via command line interface.
"""
import argparse
import os
from io import BytesIO
from urllib.request import urlopen
from zipfile import ZipFile
from deepreg import log
logger = log.get(__name__)
def download(dirs... |
e16917252759ede3023d1839abf6e555b47dbf153ed7391b8823fb8a29456efa | Python | 2,634 | 59 | import gc
import runpy
from pathlib import Path
from unittest.mock import patch
import pytest
from qtpy.QtCore import QCoreApplication, QEvent
from qtpy.QtWidgets import QApplication
EXAMPLES_DIR = Path(__file__).parent.parent / "docs" / "examples"
EXAMPLES = sorted(EXAMPLES_DIR.rglob("*.py"))
@pytest.mark.parametr... |
d5caa8f75d0b9b63015974cf96e34dfd43c5d89cef919b892013609e2d338977 | Python | 2,635 | 95 | """
This is ported from Matlab code from the original TDR codebase.
"""
import numpy as np
def tdrMeanAndStd(data, avgpars=None):
"""
tdrMeanAndStd compute mean and std of responses
Inputs:
data: population response (sequential or simultaneous, see 'help tdr')
avgpars.trial: logical indices of t... |
ffd9cdbf658998b241e7452e33bfd2b0982ff798b98787615dd2a06f6f0bf749 | Python | 2,635 | 48 | """A collection of tools for representing sound waveforms with spectrograms.
The contents of this package were derived from the gammatone toolkit, which is
licensed under the 3-clause BSD license. The full copyright disclaimer can be
found below, or at the following URL:
https://github.com/detly/gammatone/blob/master/... |
2e38af0be816f57f19310e550eac0a8b33dd0af6bfdabc7fbcd62895e1e14f2f | Python | 2,636 | 74 | import numpy as np
from src.wrappers.OsipiBase import OsipiBase
from src.original.fitting.OJ_GU.ivim_seg import seg
class OJ_GU_seg(OsipiBase):
"""
Segmented fitting algorithm by Oscar Jalnefjord, University of Gothenburg
"""
# I'm thinking that we define default attributes for each submission lik... |
72c904d924a2948b0a77e7212e4a96eab86d6986f0d59389704fd737391affec | Python | 2,636 | 85 | import pandas as pd
import time
import ijson
import content_feature as cf
import csv
import spacy
import copy
nlp = spacy.load('en_core_web_lg')
def get_content_vector(tweets):
links = cf.count_urls(tweets)
mentions = cf.count_mentions(tweets)
content_vector = {
"links_ratio":links[0],
"uni... |
b5b14184468015d5f0772ab1992b3542266c702cf3e35e95dbd737dd809c6c10 | Python | 2,636 | 57 | import numpy as np
from numpy.random.mtrand import RandomState
from sklearn.model_selection import StratifiedShuffleSplit
from brainscore_core.supported_data_standards.brainio.fetch import get_assembly
from brainscore_core.supported_data_standards.brainio.packaging import package_data_assembly, package_stimulus_set
... |
38eda9c3e6be1d34cd08096d1eebae72b4e312c27e93e05e608f7ead707b04b3 | Python | 2,637 | 77 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Maximilian Betz
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Li... |
7ca89213daa8e3522a62d3b9a157aade218992b8ae8e4dfa11ad6b8a467f5503 | Python | 2,637 | 72 | # -*- coding: utf-8 -*-
import numpy as np
from dipy.io.stateful_tractogram import StatefulTractogram
from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
from scipy.sparse import dok_matrix
from scilpy.tractograms.tractogram_operations import union_robust, \
intersection_robust
def filt... |
0f678dc3560e44bd557341535f08b2bd30d6366c146c504cb3dfe2bea9dd8e00 | Python | 2,638 | 68 | from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import ssl
import functools
import timm
from brainscore_vision.model_helpers.check_submission import check_models
ssl._create_default_https_context = ssl... |
36b1f59d92d60f000b73995560a22052b44ff2bb6feb2da7fbf4b6358ee7306a | Python | 2,638 | 93 | import os
from typing import Dict, List, Union
import yaml
from deepreg import log
from deepreg.config.v011 import parse_v011
logger = log.get(__name__)
def update_nested_dict(d: Dict, u: Dict) -> Dict:
"""
Merge two dicts.
https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionar... |
5563ed067f6d0c1d2e2d83dca8ee253b03e34715d52607bae0974aa0c7710c54 | Python | 2,638 | 91 | from seisbench.data.base import WaveformBenchmarkDataset
class VCSEIS(WaveformBenchmarkDataset):
"""
A data set of seismic waveforms from various volcanic regions: Alaska, Hawaii, Northern California, Cascade volcanoes.
"""
def __init__(self, **kwargs):
citation = (
"Zhong, Y., &... |
656e8556c992bd59144edb9293c26adaf8d37928c309d4ebe4463011d39b4a9a | Python | 2,638 | 65 | import csv
import pathlib
import matplotlib.pyplot as plt
import numpy as np
NANO_FACTOR = 1e9
STEADY_STATE_CURRENT = 1.09e-10 # Amperes
from helper_functions import __file__
MODULE_BASE = pathlib.Path(__file__).parent.parent
DEFAULT_DATA_PATH = MODULE_BASE.joinpath('reference_data/Miller_2026/dendritic_current')
def... |
75960ccfb46f1ac1ced0bbb9e79b80c1e920e59e9fb9fd5d0316c9106345a25a | Python | 2,638 | 74 | _base_ = ['RepLKNet-31L_22Kpretrain_upernet_160k_ade20k_640.py']
model = dict(
backbone=dict(
large_kernel_sizes=[27,27,27,13],
channels=[256, 512, 1024, 2048],
drop_path_rate=0.5,
small_kernel=None,
dw_ratio=1.5,
norm_intermediate_features=True
),
decode_hea... |
6a112aec211fe4887ed014ff24069e37f99ef31be15a9d04290c191838a850c9 | Python | 2,639 | 81 | from dataclasses import dataclass
from pathlib import Path
from typing import TYPE_CHECKING, Literal
from eir.experiment_io.configs_io import load_configs
from eir.experiment_io.io_utils import check_version
from eir.experiment_io.label_transformer_io import load_transformers
from eir.experiment_io.output_object_io im... |
826ed7b0d902b21bf26b5c03eadfd965fe4a65152ed3264a2a72bcbc6f7602dc | Python | 2,639 | 84 | # -*- coding: utf-8 -*-
"""
Created on Sat Dec 19 04:29:29 2015
@author: ckirst
"""
import os
import ClearMap.Settings as settings
filename = os.path.join(settings.ClearMapPath, 'Test/Data/ImageAnalysis/cfos-substack.tif');
import ClearMap.Visualization.Plot as plt
import ClearMap.IO as io
data = io.readData(filename... |
8e634a082df3cb59299755ae52bf5474b10845604252e510871afe2e972c9e92 | Python | 2,639 | 77 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import os
from datetime import timedelta
from pathlib import Path
from tempfile import TemporaryDirectory
from django.conf import settings
from django.test import SimpleTestCase
from django.utils import timezone
from cvat.apps.dataset_manager.cron ... |
0463cc93903790830887d9f4d03454b58e5de83266e4c62a82d84712c7e7a675 | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
46718fddc1abcc9fe7c3457a363d17f2d89b1635c03a4994e90620b794b1c204 | Python | 2,640 | 66 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Maximilian Betz
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Li... |
48ea75192a101a353435c208519e2ec2efd07fb9a1743bd8d75e692d7c506054 | Python | 2,640 | 63 | # -*- coding: utf-8 -*-
################################################################################
## Form generated from reading UI file 'delete_stream_dialog.ui'
##
## Created by: Qt User Interface Compiler version 6.4.2
##
## WARNING! All changes made in this file will be lost when recompiling UI file!
######... |
51bd23d4f67e234e9327738d94217f0180f0816d7b145ac3391fadc6c2eb20af | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
7c2b5847cad627fb40fee9097f55a320151795e96a308610e66f2570dd9db15a | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
b41bdda4917e49db924f38bec089845c47efc6a57d4e3021a06ef515824d489b | Python | 2,640 | 68 | from train_gtex import *
def main():
parser = argparse.ArgumentParser(description="Run a training experiment")
parser.add_argument("--config_path",type=str)
parser.add_argument("--fold",type=int)
parser.add_argument("--seed",type = int)
parser.add_argument("--train_gene",type = str)
parser.add... |
be357ab45df2a3b6d9260ff8a9169ce06176aca6b1888ca47a5a9a80e7b5b6ce | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
be6d1d23f4b0d18f2840e07c8c35aaf99d8fe4c7f083125d2710bc63799e095c | Python | 2,640 | 34 | from testsetclass import TestsetClass
class ISOL24(TestsetClass):
def __init__(self):
self.weak = 1.0
self.molecules = ['i5p', 'i12e', 'i18p', 'i24p', 'i22e', 'i8p', 'i9e', 'i19e', 'i22p', 'i23p', 'i12p', 'i15e', 'i8e', 'i9p', 'i2e', 'i7e', 'i21p', 'i16p', 'i18e', 'i24e', 'i5e', 'i6e', 'i4e', 'i4p... |
f8877bfffe598013a947fef793b2b5eb0b95528507be642e0aa6bf17ea2f6af1 | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
fb42b445e55966e6272181711013342b5d5809544f0cf2d4149ed564468f1717 | Python | 2,640 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
063e2b8775889a56cbf0da5a3345425d3e0f146864cbda6def135815268d639f | Python | 2,641 | 68 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
import numpy as np
import torch
from ultralytics.utils.checks import check_requirements
from .base import BaseBackend
class AxeleraBackend(BaseBackend):
"""Axelera AI inference back... |
47ae6ccf99446f16cd3329a6c92290c7b14152b1774e9662110e54c7a723fef5 | Python | 2,641 | 73 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
# Generated by Django 4.2.21 on 2025-10-14 14:50
import django.db.models.deletion
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
mi... |
7f1667f1be714c5e7711c08996523ab19e7f51a6442f16b066a8c30638a946c7 | Python | 2,641 | 135 | #!/usr/bin/python3
#
import os
import sys
import argparse
import numpy as np
from uac import utils
# Create the parser
my_parser = argparse.ArgumentParser(description="Calculation of old atrial coordinates")
# Add the arguments
my_parser.add_argument("target_path", metavar="path", type=str, help="Path for the new ta... |
10810e8c834d5491fad7f63768da87248e6d1876c8696a731f554e67c5ed611c | Python | 2,642 | 69 | import logging
try:
import faiss
except ModuleNotFoundError:
logging.warning(
"""The pytorch-metric-learning testing module requires faiss. You can install the GPU version with the command 'conda install faiss-gpu -c pytorch'
or the CPU version with 'conda install faiss-cpu -c p... |
d66f9b2c930066e91cf3fcfdf1fe7d8bf387a3a06ca4eb8263960c430f484434 | Python | 2,642 | 69 | from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import ssl
from .helpers.hmax import HMAX
from .helpers.pytorch... |
a91f9a9a27f9a1cd95a96c9adcab3e32e50cf9a87938fb9f3886f83211869e1a | Python | 2,643 | 54 | import pytest
import brainscore_vision
from brainscore_vision import load_stimulus_set
@pytest.mark.private_access
class TestMarques2020V1Properties:
@pytest.mark.parametrize('identifier,num_neuroids,properties,stimulus_set_identifier', [
('Cavanaugh2002a', 190, [
'surround_suppression_index',... |
ea3482d926ca9712ac57232ff54f71b9a7c107cf2ec9454ec91480ef02c41bfd | Python | 2,643 | 85 | import torch
from torch import sin, cos, atan2, acos
def rot_z(gamma):
return torch.tensor([
[cos(gamma), -sin(gamma), 0],
[sin(gamma), cos(gamma), 0],
[0, 0, 1]
], dtype=gamma.dtype)
def rot_y(beta):
return torch.tensor([
[cos(beta), 0, sin(beta)],
[0, 1, 0],
... |
8743e58661d4ff5433532e29de9b08f49a1e6806a8d7f38114ad7f2ba45ef5ee | Python | 2,644 | 74 | """ A dataset reader that reads single tarfile based datasets
This reader can read datasets consisting if a single tarfile containing images.
I am planning to deprecated it in favour of ParerImageInTar.
Hacked together by / Copyright 2020 Ross Wightman
"""
import os
import tarfile
from timm.utils.misc import natural... |
3c4934d663fcc219c1959bf57b7726c116e5a46f533cf1bc695d3a49686328c1 | Python | 2,645 | 92 | from abc import abstractmethod
from typing import Any
import tensorflow as tf
from tensorflow.keras.layers import (
Activation,
BatchNormalization,
Conv3D,
Dropout,
GlobalAveragePooling3D,
GlobalMaxPooling3D,
Input,
MaxPooling3D,
Reshape,
)
from tensorflow.keras.models import Model
... |
f030df4a4d5e9f8c80103f875f0aa5ab9c2a5bb2b3ce38e690aa20eb7c85dad8 | Python | 2,645 | 68 | """Test Qsci."""
import pytest
from qtpy import PYSIDE2, PYSIDE6
from tests.utils import pytest_importorskip, using_conda
@pytest.mark.skipif(
PYSIDE2 or PYSIDE6 or using_conda(),
reason="Qsci bindings not available under PySide 2/6 and conda installations",
)
def test_qsci():
"""Test the qtpy.Qsci name... |
0670a017506824b87ccb17c4afcc11d5d15a1bec17e3084e0eaf70fe6fadeaad | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
1bad800d2a385c3bb2ffe6cd53ddbbb779b7cca07dfe51ad24ae94ee3827b260 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
233cb0f14ed0239826c5c18f11b8c69cc76e54fc0542f3f58aa2dd65883035b0 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
47a3d8eb62e03fd9b59c0b3de7dce67fd1d467f4b8fc053a8f3f264f723f8f4b | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
607c966d6b64627f61ef5be053b366a93c19d9e922463c3bf536c07785411210 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
6c3ffbe2897fb4d752d0312a5889c06b559a0f10f4b566562b1cfedad0eeece1 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
96d842bb63d3f41ef2b6e75b9b44a0d2be51ce057b72e10b496a3926ded68370 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
9d3a0293117640d02890207906ccd27c013af9487a75537c69844e4f992af157 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
b19a2140b4b438879fb61bb277dd39592e69a633a1a173fb447571408e494cae | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
bd106ca45fa85211469940227e92248f2b630478c2da80dfbd9881c40d41bc90 | Python | 2,646 | 77 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
f64264794573cb73a458903c7c191a6310fd473dfa31d21d2b06374e12d24562 | Python | 2,646 | 76 | import skimage.io as skio
import numpy as np
import napari
import tifffile
import argparse
def load_image(path):
'''
Load .tif file which is generated from Amira with skimage.io
Args:
path: path of .tif file
'''
tif_stack = skio.imread(path, plugin='tifffile')
#tif_stack = tifffile.imre... |
51d7a884030c9aeee4c2b38ca19c0d69b71aa6a094f95641f3a49f788ccd26e9 | Python | 2,647 | 79 | ### Cloned from github milesial/pytorch Unet
""" Parts of the U-Net model """
import torch
import torch.nn as nn
import torch.nn.functional as F
class DoubleConv(nn.Module):
"""(convolution => [BN] => ReLU) * 2"""
def __init__(self, in_channels, out_channels, mid_channels=None):
super().__init__()
... |
608dd22d15be54821341573bd6ad6ac8d7ff0fd428449b59cd5dfaf95b79ad89 | Python | 2,647 | 84 | from unittest.mock import MagicMock
from flair.data import Sentence, Span, Token
from flair.embeddings import FlairEmbeddings
from flair.visual import *
from flair.visual.ner_html import render_ner_html, HTML_PAGE, TAGGED_ENTITY, PARAGRAPH
from flair.visual.training_curves import Plotter
def test_highlighter(resourc... |
277d8513501fadef410689b17046f8b6a5df6edafeba1ba534b105aa8945baa2 | Python | 2,648 | 103 | # -*- coding: utf-8 -*-
# external inputs
import numpy as np
from numpy.fft import fftshift
def filter_bold_2d(nx, ny, fovx, fovy, fwhm, beta):
"""Filter BOLD 2D.
This defines the BOLD blurring in 2D. It is defined as modulation transfer
function in spatial frequency space. The filter is the Fourier tr... |
bde8bd2c8d57521ec766e8e35b751c877101cb19d8fc3066780a1973a2c02d9b | Python | 2,648 | 83 | # The ImpedanceFitter is a package to fit impedance spectra to
# equivalent-circuit models using open-source software.
#
# Copyright (C) 2018, 2019 Leonard Thiele, leonard.thiele[AT]uni-rostock.de
# Copyright (C) 2018, 2019, 2020 Julius Zimmermann, julius.zimmermann[AT]uni-rostock.de
#
# This program is ... |
5e91cdcb13086b5212d0e8c374e69304c1a87f209faae9655141696a056a0f8a | Python | 2,649 | 62 | from brainscore_vision.model_helpers.check_submission import check_models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torchvision
import antialiased_cnns
import functools
import torch
import ... |
b383ab0d87cdd87e202929df5ac04cfd984410c0f3ea02242289f3e5085f4763 | Python | 2,649 | 71 | # Requirements (tested with TensorFlow 2.16.1):
# pip install numpy tensorflow
import numpy as np
import os
from tensorflow.keras.models import load_model
# === PARAMETERS ===
NUM_OUTER_FOLDS = 9
NUM_INNER_FOLDS = 8
MODEL_DIR = "saved_models" # Change if your directory is different
MODEL_PREFIX = "model"
... |
e45ed685e29565c505b842abc257974e7b5f50863c7fa4bc2cd17e8c3f78f253 | Python | 2,649 | 83 | """
Code adopted from https://github.com/SuperElastix/elastix_napari
Author: Viktor van der Valk, v.o.van_der_valk@lumc.nl
"""
import tempfile
from pathlib import Path
from typing import Optional
import itk
import numpy as np
_ELASTIX_PARAM_FILES = [
# Path(__file__).parent / "Par0033similarity.txt",
# Path(_... |
94d4e3afa260296777869e206e52918aa0da585f3dcc9261a2af9c09f07a2e48 | Python | 2,650 | 93 | import torch
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
#below code was adapted from https://github.com/nairouz/R-GAE/tree/master/GMM-VGAE here. We thank for the authors to make it publicly available
def parse_index_file(filename):
"""Parse the index file path
Ar... |
13d8a19b8b119bc132956359411d048dd0b1831e74e5e12ff05775548b34d2d7 | Python | 2,651 | 78 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
1f653b104f3fbeb058bcb7d5a28aebe6724ecf5b1d454563b9af191e9d7ec38a | Python | 2,651 | 78 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
637757e2f361e4988ef63caf382a78036ba029c803bfd8ea1ecfd469bbe682c2 | Python | 2,651 | 78 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import os
from urllib.request import urlretrieve
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_prepro... |
2966a4018e3f105f393fabffdf32bd3dee190beec03d031d2927e2efcff43a94 | Python | 2,652 | 77 | from abc import ABC, abstractmethod
from typing import Any
class Registrator(ABC):
# TODO probably the init here should be removed?
# def __init__(self, backend):
# self.backend = backend
@abstractmethod
def register(
self,
fixed_image_path: Any,
moving_image_path: Any... |
462cbff20005320673e306abaaf57e8a54b6ec988f8786cd315e13986d19f263 | Python | 2,652 | 136 | #! /usr/bin/env python
# aponteeduardo@gmail.com
# copyright (C) 2017
''''
Automatically generate the necessary functions.
'''
def gen_code_n_states(f, p):
fname = 'c_{0:s}_n_states_{1:s}.c'.format(f, p)
code = '''/* aponteeduardo@gmail.com */
/* copyright (C) 2018 */
#include "mexutils.h"
void
mexFu... |
5f8cc1d0e5e633c3cea323daa6752bc20b4103d2c7424f99f1d22ea4470b52b0 | Python | 2,652 | 59 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 27 10:53:04 2020
@author: Cristian
"""
import numpy as np
import pandas as pd # (not used below, but kept if you need it elsewhere)
# Pattern duration: 2 seconds (informational only; not used by the code)
# Number of EC neurons in the p... |
83476dc75b514980e3db0d903b30cd239d2af73612952a6d20555b0569bf7b95 | Python | 2,652 | 122 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import celldancer as cd
import anndata
TLS_path = '/data/processed/TLS.h5ad'
# In[6]:
TLS = anndata.read_h5ad(TLS_path)
TLS.obs_names_make_unique()
N, G = TLS.shape
# In[10]:
data_path = '/VeloVAE/celldancer/data'
# In[11]:
dataset='TLS'
# In[12]:
df ... |
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