sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3ad0e39b11fcce88b63b878f1a01e652c4a703c5a1bd6f097d38233c1b82b428 | Python | 1,368 | 54 | import argparse
from datetime import datetime
from deepreg.train import train
name = "paired_mrus_brain"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
"--te... |
a28cdf98091a881f1a77d21ac07c12d362f97be5738d65eb788bead2afcaeffa | Python | 1,368 | 45 | from dataclasses import dataclass
from typing import TYPE_CHECKING
import torch
from torch import nn
if TYPE_CHECKING:
from eir.setup.output_setup_modules.tabular_output_setup import (
al_num_outputs_per_target,
)
@dataclass
class LinearOutputModuleConfig:
pass
class LinearOutputModule(nn.Modu... |
24b4c1b10b4df3a10928fbd8e54806da5b6c521a26cfafbebd792baff6cb386d | Python | 1,369 | 51 | """This script provides an example of using custom backbone for training."""
import tensorflow as tf
from deepreg.registry import REGISTRY
from deepreg.train import train
@REGISTRY.register_loss(name="root_mean_square")
class RootMeanSquaredDifference(tf.keras.losses.Loss):
"""
Square root of the mean of squ... |
2b3d01f2574ee04bad6388d3a126efb8e399eaabcdf8309d05178b5ee43bb638 | Python | 1,369 | 50 | # -*- coding: utf-8 -*-
"""
Created on Fri Nov 24 23:06:03 2023
@author: Artur Klepaczko
"""
from pathlib import Path
import random
from tqdm import tqdm
npy_root = Path(R'D:\TexturesKidneys\NPY_v2')
exp_root = Path(R'D:\TexturesKidneys\OnePatientOut')
patients = []
for category_dir in npy_root.iterdir():
for ... |
8a87b1e5f6f17275dd570be4b4bfc0816d3d5dfc794aac7d8192a3b88463edd1 | Python | 1,369 | 43 | import os
import logging
import torch
import numpy as np
import torchio as tio
def load_ivim_subject(study_subject_path):
"""
loads torchio subject with IVIM data (signals and bvalues)
Args:
study_subject_path: path in which subject data is located
Returns:
"""
subject_dict = {}
... |
f292a22742f1ff4fb9118ddb908aa89897d7378225332212222b926c0e7c5e0d | Python | 1,369 | 36 | from pathlib import Path
import pytest
from pytest import approx
from brainscore_core.supported_data_standards.brainio.assemblies import BehavioralAssembly
from brainscore_vision import load_metric
from brainscore_vision.benchmarks.rajalingham2018.benchmarks.benchmark import load_assembly
@pytest.mark.private_acces... |
01377c95337cc50ecb94c2991c0badd81e210f170829ebfaecbcb263ae514bb6 | Python | 1,370 | 54 | #!/bin/env python
import numpy as np
import sys
xmin = float(sys.argv[1])
xmax = float(sys.argv[2])
ymin = float(sys.argv[3])
ymax = float(sys.argv[4])
zmin = float(sys.argv[5])
zmax = float(sys.argv[6])
nx = int(sys.argv[7])
ny = int(sys.argv[8])
nz = int(sys.argv[9])
area_tot = (xmax-xmin)*(ymax-ymin)*(zma... |
56c0df93b9b828eb34a207148e925b9b2201da41fa329634e2ceb2e4f804dc28 | Python | 1,370 | 45 | import os
import numpy as np
import scipy.sparse as sp
import torch
from six.moves import cPickle as pickle
from torch_geometric.data import Data
from torch_geometric.utils import to_undirected, remove_self_loops
from preprocessing import load_data
import pandas as pd
from collections import Counter
df = pd.read_csv... |
1df0b6ae61c0e8330998f55d8a0f4bd1fd47e807d3400d8ec3de1c2ee301e0ab | Python | 1,371 | 49 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides Qt3DLogic classes a... |
312becc18db80b48bfa3d6dc2ef2937178b09a1ac6463b2c60484c5119b5eb3a | Python | 1,371 | 60 | #!/usr/bin/env python3
import argparse
import numpy as np
from ase.io import read, write
from KerNNCalculator.KerNNCalculator import *
import argparse
from os.path import splitext
from ase.vibrations import Vibrations
'''
Usage: python ase_vibrations.py -i structure.xyz
'''
#parse command line arguments
parser = ar... |
426ee7bd9bd49f3b56cab0fc4741b7512002f198dd899215d8d35b9887c3d762 | Python | 1,371 | 49 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides Qt3DInput classes a... |
ca39b951944992d100212d06b6e08750c5b17677c57fecb2b8b736774e77a5e5 | Python | 1,371 | 49 | from numpy import arange
def get_grid():
zmin = 0.4
zmax = 4.4
dz = 2
assert zmax <= 6
assert zmin >= 0.3
assert zmax >= zmin + dz
ymin = -7
ymax = -4
dy = 0.5
assert ymax >= ymin + dy
assert ymax <= -4
as... |
0b1bdd3f76a18a6aa3db42738eafa212d8c1b0cab6fa5621cfae82caf4878c53 | Python | 1,372 | 74 | # -*- coding: utf-8 -*-
"""TODO"""
import os
import sys
from mpi4py import MPI
from core.logger import Logger
from core.system import System
logger = None
kernel = None
mpicomm = None
def init(directory='.', simulation_name='default', logfile_prefix='default', quiet=False):
"""TODO"""
# Initialize MPI and... |
339ff0b2e36b4b6c3a60045fb1cf7fcedc2fde2492a87e537a351f0f46575a87 | Python | 1,372 | 55 | import argparse
from datetime import datetime
from deepreg.train import train
name = "paired_mrus_prostate"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
"... |
3d722e843563ad621a9f90a2807db2b80226310c0f536242dce9d24a2ae5ac31 | Python | 1,372 | 45 | """ Separate overlapping surfaces """
import SVMTK as svm
from pathlib import Path
# TODO : improve
if __name__ == "__main__":
print("Start ",__file__)
outdir = Path("results")
outdir.mkdir(exist_ok=True)
sphere1 = svm.Surface()
sphere2 = svm.Surface()
# Create two spheres
# First... |
83be8a92556134506f13dec63067c82ba239d2029d5f3885e82c90bc2efc65e9 | Python | 1,372 | 40 | from setuptools import setup, find_packages
with open("README.md", "r", encoding="utf-8") as fh:
long_description = fh.read()
# with open("requirements.txt", "r", encoding="utf-8") as fh:
# requirements = [line.strip() for line in fh if line.strip() and not line.startswith("#")]
setup(
name="harvest",
... |
26d8ed27de54ce6f9897245d34bd30d36f75c71359a4eba78972d4e4fea6d3e1 | Python | 1,373 | 39 | # -*- coding: utf-8 -*-
import os
import nibabel as nib
import numpy as np
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
from scilpy.reconst.utils import is_data_peaks
def test_is_data_peaks_with_real_data():
fetch_data(get_testing_files_dict(), keys=['processing.... |
3672922946fd967ec7c60808fe8f6a0c91ce593adcf3ac494c69990a5908f4ad | Python | 1,373 | 43 | import functools
import socket
from datetime import datetime
from pathlib import Path
from neuralib.tools.slack_bot import send_slack_message
from neuralib.typing import PathLike
__all__ = ['slack_bot']
def slack_bot(*, env_file: PathLike | None = None, timestamp: bool = True):
"""sending error message to slack... |
98955939bd76e8808a3a2fa73b39266b591f14ac7295943a0239d14cb12379c8 | Python | 1,373 | 40 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("quality_control", "0012_qualityrequirement_and_more"),
]
operations = [
migrations.AlterField(
model_name="q... |
00b7464d47e4ae8ddc2957b52deb050a35da75603c59b6a025ff4e41ca3f94dd | Python | 1,374 | 62 | """Train an HMM.
"""
from sys import argv
if len(argv) != 3:
print(
"Please pass the number of states and run id, e.g. python 2_train_hmm.py 8 1"
)
exit()
n_states = int(argv[1])
run = int(argv[2])
output_dir = f"results/models/{n_states:02d}_states/run{run:02d}"
print("Importing packages")
im... |
88d2d70431b89255d9f185c654c70373a02e9e44a8c3e8b3e7e3fca94672f2ee | Python | 1,374 | 48 | """Run molecular docking through the ChemGraph agent.
Docks a small-molecule candidate into a receptor with AutoDock Vina using the
``molecular_docking`` workflow, which binds the docking tools and prompt for you. The
candidate can be a SMILES, a molecule name, or a PubChem CID; the receptor here is the
prepared vanco... |
2a357918c34b6c4fe17c255dbcf20b98c01118ea97c8f57eb9e7d74e47d17524 | Python | 1,375 | 54 | import sys
import numpy as np
import hipsternet.neuralnet as nn
import hipsternet.solver as solver
time_step = 10
n_iter = 1000000000
alpha = 1e-3
print_after = 1000
H = 64
if __name__ == '__main__':
with open('data/text_data/japan.txt', 'r') as f:
txt = f.read()
X = []
y = []
... |
a67e632fd190bc05d634a6e0ebba3428fbb2e9411ee1552d4cd81b2f218e38fd | Python | 1,375 | 41 | """
(C) IBM Corp, 2019, All rights reserved
Created on Aug 25, 2019
@author: EHUD KARAVANI
"""
import unittest
import pandas as pd
import numpy as np
from causallib.estimation import MarginalOutcomeEstimator
class TestMarginalOutcomeEstimator(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls... |
b1d5208bc8dadb9ef0f16745e79a829d34df4a380c2675b2cf6095fa2ed676af | Python | 1,375 | 41 | #!/usr/bin/env python
"""
HAL module for emulating a (IR) laser for the focus lock.
Hazen 04/17
"""
import storm_control.hal4000.halLib.halMessage as halMessage
import storm_control.sc_hardware.baseClasses.amplitudeModule as amplitudeModule
class NoneIRLaserFunctionality(amplitudeModule.AmplitudeFunctionality):
... |
31684f11cb1a2f176902898a05144a0f21851e53c48699bc6d64918209e87561 | Python | 1,376 | 51 | #!/usr/bin/python3
#
EPSILON = 100
EPSILON_ABC = 0.025 * 0.01
# 21: LSPV. 23: LIPV. 25: RSPV. 27: RIPV
# inferior PV parameters
R1_23_27 = 0.06 # x_rad of inf PV
XSHIFT_23 = 0.07 + R1_23_27 # x_cen of LIPV
XSHIFT_27 = 1 - XSHIFT_23 # x_cen of RIPV
R2_23_27 = 2 * R1_23_27 # y_rad of inf PV
YSHIFT_23_27 = 0.63 #... |
85fd74fafdebebf3d6ff8386d48343d9ff708b39233985a6f1e280a40ab59476 | Python | 1,376 | 41 | import torch
import numpy as np
from utilities.ivim.forward_model import ivim_parameters_to_signal
def simulate_ivim_signal(D, Dp, f, S0, bvalues, SNR_array, rg):
"""
simulate ivim signal
Args:
D: diffusion coefficient
Dp: pseudo diffusion coefficient
f: perfusion fraction
... |
8cb4acb98f029caebf9b9a3fdb6bdc90d5b18fb6d29d47f8694232e16df2849a | Python | 1,376 | 44 | from __future__ import annotations
import random
from dataclasses import replace
import numpy as np
from napari.qt.threading import FunctionWorker
from pytestqt.qtbot import QtBot
from brainways.pipeline.brainways_params import BrainwaysParams, TPSTransformParams
def randomly_modified_params(params: BrainwaysParam... |
ae55c061ec40536e9cd797545abe44364655f9d966ba99fc864931b41fde539e | Python | 1,376 | 53 | import argparse
from datetime import datetime
from deepreg.train import train
name = "unpaired_ct_lung"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
"--tes... |
f1cc27703fd86bda18c70f351a2301c2642ca7de6d5ccda1c9d038f129c65c7b | Python | 1,376 | 53 | import argparse
from datetime import datetime
from deepreg.train import train
name = "grouped_mr_heart"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
"--tes... |
6afac09a8ff36ce7c5a7b5cf80c454ed335714503e939e632427960bd2c81346 | Python | 1,377 | 40 | import os.path as op
import dipy.core.gradients as dpg
import dipy.data as dpd
import nibabel as nib
import nibabel.tmpdirs as nbtmp
import numpy.testing as npt
import pytest
from AFQ.models import dki
from AFQ.utils.testing import make_dki_data
def test_fit_dki_inputs():
data_files = ["String in a list"]
b... |
c2e7187808189d53885aa9512f71a5dec6093aa42bb0f09b0468c68bc08d19f4 | Python | 1,377 | 52 | """
This module implements the proximal operator.
"""
import torch
import torch.nn as nn
from typing import Tuple
from deepdwi import util
from deepdwi.dims import *
class VAE(nn.Module):
def __init__(self,
model: nn.Module):
super(VAE, self).__init__()
self.model = model
... |
43b4fff075a6e39581a611a594d46f4411e80fb1c8c9684027b9007e3a5da991 | Python | 1,378 | 44 | import unittest
from unittest import mock
from ogo.cli import GenerateFEM
class TestGenerateFEM(unittest.TestCase):
def setUp(self) -> None:
pass
def tearDown(self) -> None:
pass
@mock.patch("ogo.cli.GenerateFEM.spine_compression_main")
def test_dispatch_to_vertebra(self, mock_spine)... |
4d23056f243026fcafde5c506648aa018cfae44c01d7d47db6cb2713b737f271 | Python | 1,378 | 39 | from typing import Optional
from torch import nn, Tensor
import torch.nn.functional as F
import torch
__all__ = ["FocalCosineLoss"]
class FocalCosineLoss(nn.Module):
"""
Implementation Focal cosine loss from the "Data-Efficient Deep Learning Method for Image Classification
Using Data Augmentation, Focal ... |
5ec4bb65c2cfe337fa933d30e636d94ddbefbe8e93b2c8b30960dee5719e3ea1 | Python | 1,378 | 40 | from qtpy.QtCore import Signal
from qtpy.QtWidgets import QGraphicsView
class QGraphicsViewMT(QGraphicsView):
#: Emitted when the mouse moves over the view.
mouseMoved = Signal()
#: Emitted when the mouse enters the view.
mouseEntered = Signal()
#: Emitted when the mouse leaves the view.
mouseL... |
6707116f0b49854947c4138c0ad0d3e27c9b5d2af21be27c331f8191399bca3b | Python | 1,378 | 45 | import csv
import numpy as np
import matplotlib.pyplot as plt
import yaml
import sys
import os
import h5py
pathpath = 'PATHS/filepaths_carlen.yml'
with open(pathpath, 'r') as myfile: pathdict = yaml.safe_load(myfile)
sys.path.append(pathdict['code']['workspace'])
from pfcmap.python.utils import tessellation_tools a... |
92f4b2661fc05390f6b1d1f5fdd151fc997faf94b7304d8ba3ee1243929d1a57 | Python | 1,378 | 34 | from utils import setup_features
from param_parser import parameter_parser
from utils import tab_printer, read_graph
import numpy as np
import pandas as pd
from sgcn import SignedGCNTrainer
from param_parser import parameter_parser
from utils import tab_printer, read_graph, score_printer, save_logs, read_st_graph, trai... |
ace20c7a47fbc044074bdb4ae935c9a15ce4eec9e90c4ecb88741cc14322771c | Python | 1,378 | 45 | # -*- coding: utf-8 -*-
"""Check correct synchronization with trigger signal."""
import matplotlib.pyplot as plt
import numpy as np
import scipy.io as sio
__all__ = ["check_trigger"]
def check_trigger(input_biopac):
"""This function loads the digital input from a saved biopac mat-file and checks the
number ... |
b192d27d2aa3e748854490ce4a89bc22402a930397f565207c2edb55f1e48257 | Python | 1,378 | 30 | #--------------------------------------------#
# 该部分代码用于看网络结构
#--------------------------------------------#
import torch
from thop import clever_format, profile
from torchsummary import summary
from nets.deeplabv3_plus import DeepLab
if __name__ == "__main__":
input_shape = [512, 512]
num_classes =... |
fddbbe551069d1ae887b9171d1f3b595e990fb21fa89ff414c239c7b3dc29619 | Python | 1,378 | 54 | import argparse
from datetime import datetime
from deepreg.train import train
name = "unpaired_mr_brain"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
"--t... |
6423e8f2a293aa1beca5c9dd3b62ec3330d050a274a6821f901d65c2aeadde71 | Python | 1,379 | 38 | from nipype.interfaces.fsl import Reorient2Std
from PUMI.engine import BidsPipeline, NestedNode as Node
from PUMI.pipelines.anat.anat_proc import anat_proc
from PUMI.pipelines.func.compcor import anat_noise_roi, compcor
from PUMI.pipelines.anat.func_to_anat import func2anat
import os
from PUMI.pipelines.func.temporal... |
8a0bfe452767e67027c0579fd19a3497b3201b512cbfab893b3539897e5b5d7a | Python | 1,379 | 60 | import numpy as np
from impedancefitter.cpe import cpe_ct_model, cpe_ct_w_model, cpe_model
omega = 2.0 * np.pi * np.logspace(1, 8, num=20)
k = 1e-7
alpha = 0.9
Rct = 100
Aw = 10
def test_cpe_ct_w_type():
"""Test CPE return type."""
Z = cpe_ct_w_model(omega, k, alpha, Rct, Aw)
assert isinstance(Z, np.nd... |
014dc0c367c159571693016609d49b64dc40af50c654a97846e9ad32d616050f | Python | 1,380 | 43 | '''
dynamic import model
'''
import importlib
def import_model(model_path):
# 获取模块路径和类名
module_path, class_name = model_path.rsplit('.', maxsplit=1)
# 1 利用字符串导入模块
module = importlib.import_module(module_path)
# 2 利用反射获取类名
cls = getattr(module, class_name)
# 3 生成类的对象
# obj = cls()
... |
139842a4433f212c946722d53f94ff009156a139d6293d347b9737cac72433cc | Python | 1,380 | 49 | from ..qt import *
from .. import thalamus_pb2
from ..task_controller.util import create_task_with_exc_handling
class SpikeGlxWidget(QWidget):
def __init__(self, config, stub):
super().__init__()
layout = QVBoxLayout()
layout.setAlignment(Qt.AlignmentFlag.AlignTop)
self.setLayout(layout)
edits ... |
456f205538b5d92399c92154edac30ea92931fd4d93ab53c5f31a033691b9d98 | Python | 1,380 | 49 | # -----------------------------------------------------------------------------
# Copyright © 2009- The Spyder Development Team
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
# -----------------------------------------------------------------------------
"""Provides Qt3DExtras classes ... |
eb9c150f3ff518813b8c576e1bccdbc197cc08d96f080c3281987ec0d910156f | Python | 1,380 | 47 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import inspect
from abc import ABC, abstractmethod
from django.conf import settings
from django.core.exceptions import ImproperlyConfigured
from django.utils.module_loading import import_string
class IEmailValidator(ABC):
@abstractmethod
d... |
33bfa81ec68a74217cd11d52638b3b6b1e62a5d3f1178f81075e5e2e9a42d993 | Python | 1,381 | 48 | # -*- coding: utf-8 -*-
# python standard library inputs
import os
# external inputs
import nibabel as nb
def include_pial_correction(path, sub):
"""Include pial correction.
This function takes manual corrections from the file pial_edit.mgz which
shall be located in the freesurfer mri folder and inclu... |
de3860158aa04650faa08c4914089df8f4573643b2e354b37fe14ca65011f352 | Python | 1,382 | 34 | """M/EEG processing pipeline.
This subpackage provides a complete pipeline for processing M/EEG data from
raw sensor recordings to parcellated source-space time courses.
Modules
-------
- :py:mod:`~osl_dynamics.meeg.maxfilter` — Wrapper for Elekta Maxfilter
(SSS/tSSS).
- :py:mod:`~osl_dynamics.meeg.amm` — Adaptive ... |
09a902f6ac765631094c9c59c792e21a89f284acb57a942d9a03646a7779f27f | Python | 1,384 | 36 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/... |
46554b2cb810f52cf9ccf67d89d2a08e00a94fe81d4be7652a2f31f8e2ceac3e | Python | 1,384 | 26 | import mne
from rsatoolbox.data import TemporalDataset
from rsatoolbox.rdm import calc_rdm_movie, combine
from joblib import Parallel, delayed
from scipy.signal import savgol_filter
subs = [f"sub-{(i+1):02}" for i in range(20)]
ordered = ["square", "rectangle", "isoTrapezoid", "parallelogram", "losange", "kite", "righ... |
1edf861f03193406f8960f4610201d3f8df0d6c3cf46336619f97bd2b2532340 | Python | 1,385 | 55 | import argparse
from datetime import datetime
from deepreg.train import train
name = "unpaired_us_prostate_cv"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_argument(
... |
4172cff32ef71e82e069fe3a8e1dab7133a9a948c208a16a6cebba4a83a5fe3e | Python | 1,385 | 42 | #!/usr/bin/env python
"""
HAL module for emulating an illumination filter wheel.
Hazen 04/17
"""
import storm_control.hal4000.halLib.halMessage as halMessage
import storm_control.sc_hardware.baseClasses.amplitudeModule as amplitudeModule
class NoneFilterWheelFunctionality(amplitudeModule.AmplitudeFunctionality):
... |
6326594bf4bc9048055eeadc9dcf2059d95251371ce6d8c5945cbae80bb2ddbc | Python | 1,385 | 45 | import numpy as np
import torch
import torchio
from torchio.transforms import Transform
class SortSignalOnXval(Transform):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def apply_transform(self, subject):
"""
Sorts signals and xvals on ascending xvals
Args:
... |
c095274c30d8a7b960eccb03f2ad202dd4ef7f762dd553bceb1e2c8864768aa8 | Python | 1,385 | 26 | import os
from nipype.interfaces.base import (CommandLineInputSpec, CommandLine, traits, TraitedSpec, BaseInterface, BaseInterfaceInputSpec, File)
from traits.api import Directory, Str, List, Bool, Enum, Int, Float, TraitError, Either
class SimpleN4BiasFieldCorrectionInputSpec(CommandLineInputSpec):
input_image = ... |
edc88858aef2ef93b9098c76403bb331fe2e4dfdfca978f6fe10062d7e192b48 | Python | 1,385 | 42 | import os
import random
import torch
import numpy as np
import pandas as pd
from utils import process_data, dataloader_generation_pred, model_performance_test, metrics, parse_arguments, load_model, process_and_predict, save_results
from model import Cross_Attention_DDG, apply_masked_pooling, SinusoidalPositionalEncodi... |
73859a4ca3fb97b52273c3c98e7e5aaa82a082c72a24d6aec1080e6174cd4825 | Python | 1,386 | 36 | import pandas as pd
import argparse
from tqdm import tqdm
parser = argparse.ArgumentParser(description='Preprocess edge list')
parser.add_argument('--atlas_groups', help='Atlas Groups - List to be processed.', required=True)
parser.add_argument('--atlas_nodes', help='Atlas Node List to be processed.', required=True)
a... |
bbd50b656c351d439107e829effd7183bd8fbfb69b5784984727ec8b81837aef | Python | 1,386 | 51 | # -*- coding: utf-8 -*-
# external inputs
import numpy as np
import scipy.io as sio
import matplotlib.pyplot as plt
def check_trigger(input_biopac):
"""Check trigger.
This function loads the digital input from a saved biopac mat-file and
checks the number of sent triggers and the time difference be... |
f01e71f6600cd8f369725490b4651807963fe4f8b9df652ac8b8f9287f485d10 | Python | 1,386 | 62 | import os
from pathlib import Path
import requests
script_dir = os.path.dirname(os.path.abspath(__file__))
def download_from_zenodo(url: str, output_path: str):
response = requests.get(url)
response.raise_for_status()
with open(output_path, 'wb') as f:
f.write(response.content)
print(f"Do... |
fade159e3fb3a0ed32ee7d62b5300b76965a09c00f6ba57578e17bb55bce7fff | Python | 1,386 | 38 | """
@author: Erik Kubaczka
"""
import torch
from torch.utils.data import DataLoader
import my_setup
from data_processing.masked_sequence_model_token_based_triplet_dataset import Sequences, SequenceToSequenceDataset
def split_data(dataset, split=None):
if split is None:
split = [0.7, 0.15, 0.15]
tr... |
fc1364300acab3f52203510e20672838d4d5ef35deccb2bef054f3bf4210294e | Python | 1,386 | 41 | import os
import glob
import numpy as np
import pandas as pd
import scanpy as sc
import seaborn as sns
import matplotlib.pyplot as plt
from submodule_activity import plot_module_heatmap
adata = sc.read_h5ad('../adata_U54_BA9_splotch_lambdas.h5ad')
adata.obs['array'] = [x.split('/')[-2] for x in adata.obs.index] # d... |
2919e022b00fa19a7f1a464151edd2194393535ecc776678bf09196d9e961e68 | Python | 1,387 | 40 | # %%
# imports
# you must activate the conda env /home/data/eccolab/CondaEnvs/pymeshlab to run this script
import os
import pymeshlab
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
base_mesh_dir = '/archival/projects/SPLaT/data/mesh'
# %%
# Argle parser
parser = ArgumentParser(
prog='combine_do... |
2ab76cbaf646003ebd8ca31dbcf4c3dfa884464ad7a0606d738b5ac55a4b705a | Python | 1,387 | 62 | #!/usr/bin/env python3
import arbor as A
from arbor import units as U
from util import plot_spikes
# global parameters
# cell count
N = 10
# total runtime [ms]
T = 1000
# one interval [ms]
t_interval = 10
# numerical time step [ms]
dt = 0.1
class unconnected(A.recipe):
def __init__(self, N) -> None:
sup... |
5db7313802b8fde85446f86982b6c0e889bdf4c7d91dc001cfc75a4e69c96031 | Python | 1,387 | 40 | import numpy as np
from skimage.transform import ProjectiveTransform
from typing import Union, List
def fitGeoTrans(src: Union[List[int], np.ndarray],
dst: Union[List[int], np.ndarray],
mode="projective",**kwargs) -> np.ndarray:
"""
This function is the same as matlab fitgeot... |
ce500475f6338cf7b079492c7541980e49d2eeb6e961698fca8fdeae49441e79 | Python | 1,387 | 45 | import os
from PUMI.pipelines.anat.segmentation import defacing
from nipype import IdentityInterface
from PUMI.engine import BidsPipeline
from PUMI.engine import NestedNode as Node
ROOT_DIR = os.path.dirname(os.getcwd())
input_dir = os.path.join(ROOT_DIR, 'data_in/pumi-unittest') # path where the bids data is locate... |
e73bcee3d25baa3a2e9210ea1cab3918057b481c02e76319f11fc763340b2e8a | Python | 1,387 | 54 | import base64
from copy import deepcopy
from io import BytesIO
import requests
from PIL import Image
def encode_image_to_base64(file_path: str) -> str:
with Image.open(file_path) as image:
buffered = BytesIO()
image.save(buffered, format="JPEG")
return base64.b64encode(buffered.getvalue()... |
1cc0df39b0b9fd211e8115984d85ff634c9f9b1f4274924f6dbf1e50a0c564e0 | Python | 1,389 | 41 | import torch
import random
import h5py
import numpy as np
def set_seed(seed, device_id='cuda:0'):
# Set seed for Python's built-in random library
random.seed(seed)
# Set seed for numpy
np.random.seed(seed)
# Set seed for PyTorch CPU
torch.manual_seed(seed)
if torch.cuda.is_available():
... |
25259b1b68ac6c6add9ccd6a5d57c2790d83cab6f763ef8d53ca858273d9dcf8 | Python | 1,389 | 39 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from .load_model import *
# This is... |
3b0d81f902a0511cbb92d54d0a6499e3df9b8d2ee3c596d7abe6e01e16785823 | Python | 1,389 | 39 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from .load_model import *
# This is... |
446ed1374aa1989437e820edbbb8a56f4c7c8e0aeb6b7f95a85b725e95b75cd9 | Python | 1,389 | 61 | # -*- coding: utf-8 -*-
"""
Interface to write binary files for point like data
The interface is based on the numpy library.
Example:
>>> import os, numpy
>>> import ClearMap.Settings as settings
>>> import ClearMap.IO.NPY as npy
>>> filename = os.path.join(settings.ClearMapPath, 'Test/Data/NPY/points... |
da6a8dd2762a553e4100aee6c41393f4db2108747c8c2a85d562dd52a4e6b628 | Python | 1,390 | 36 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
09947537e2fb3ef2c377ee5c24196d797c31c327707ff7ace9380ed6d2a62f8d | Python | 1,391 | 52 | # -*- coding: utf-8 -*-
"""
Gradient nonlinearity correction
This scripts calls the HCP toolbox to correct for gradient nonlinearities in the
input volume. Further explanations can be found in a separate readme. The script
needs an installation of fsl.
Dependencies:
- gradunwarp: https://github.com/Washington-Univers... |
12bf1c4b214ca82e5e0f24c8d679ad768b7b70f48730b6b60bb984ade54a4876 | Python | 1,391 | 39 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import torchvision.models
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
from .load_model import *
# This is... |
b315382bbb86a911bc669c12519b453d5e2ead816cfc23d1fd281d048aa03da1 | Python | 1,391 | 51 | from importlib import metadata
BASE = """
Acknowledgements
================
This project would not have been possible without the people developing,
maintaining and releasing open source projects online. Therefore, I would like
to thank the people that developed the packages this project
directly depends on, those th... |
be747946bafd82ba6618c651a6defa5ca25c5551b84b11ef50c5abe2aa3b32d2 | Python | 1,391 | 38 | # SPDX-FileCopyrightText: Copyright © Timo Koch
# SPDX-License-Identifier: GPL-3.0-or-later
import matplotlib.pyplot as plt
import numpy as np
import glob
import click
@click.command()
@click.option('--folder', default="../build-cmake/app", help='Folder containing the data')
@click.option('-n', "--number-of-plots", d... |
dc073a4ec9d02fcfa8dcbe9ad544e850a6a90b0be11998318813686791444d55 | Python | 1,391 | 54 | import numpy as np
import pytest
from napari_dmc_brainmap.results.results_helpers.results_quantifier import (
ResultsQuantifier,
)
def test_majority_hemisphere_uses_left_positive_atlas_direction():
assert ResultsQuantifier._majority_hemisphere(
np.array([571, 600, 500]),
570,
) == 'left'
... |
6d4a8b57c60ecd7cf095f402921491a37766711eda66411bbad9d13e598f7be3 | Python | 1,392 | 59 | """
Motion correction workflows
to consider
-----------
- single contrast and double contrast data (vaso), interleaved?
- afni, fsl and spm, (ants mc??)
- check fmriprep for ref volume generation
- for double contrast first mc each contrast tham register both contrasts and combine transformations?
"""
from nipype.pi... |
7cdf77d66495b677ede43bbccfbc8b9bb9ebedaeb6d3a04d59f5288da36119f0 | Python | 1,392 | 52 | import arbor as A
import matplotlib.pyplot as plt
from matplotlib import cm, colors
from pathlib import Path
import numpy as np
ex = 1
ey = 0
ez = 0
def plot_morphology(mrf, *, fg=None):
tree = mrf.segment_tree
cs = cm.viridis
fg = plt.figure(figsize=(10, 10))
ax = fg.add_subplot(projection="3d")
... |
8ca7c4adedcf8233aa9b5b10762f0c5588f83715144f9d1e0ccec701b9e72455 | Python | 1,392 | 45 | from qtpy import QtGui, QtWidgets
from qtpy.QtCore import Qt, QRect
class ModeToggle(QtWidgets.QPushButton):
def __init__(self):
super().__init__()
self.setCheckable(True)
self.setMinimumWidth(44)
self.setMinimumHeight(132)
def paintEvent(self, event):
if self.isChecke... |
396711368b84cdac83aa47844910c71428244c4af9393a711c04106d43dd9373 | Python | 1,393 | 48 | #encoding=utf-8
from __future__ import print_function, unicode_literals
import sys
sys.path.append("../")
import jieba
jieba.load_userdict("userdict.txt")
import jieba.posseg as pseg
jieba.add_word('石墨烯')
jieba.add_word('凱特琳')
jieba.del_word('自定义词')
test_sent = (
"李小福是创新办主任也是云计算方面的专家; 什么是八一双鹿\n"
"例如我输入一个带“韩玉赏鉴”的标题，在自... |
3dcb5418e627762634d74eb05b40d78d7f9e67dc04fff523ee9f5ffdeed8b80c | Python | 1,393 | 35 | """
TMS Explorer was developed to assist with the data preprocessing of transcranial
magnetic stimulation (TMS) as part of the study "Transcranial direct current
stimulation (tDCS) and mindfulness meditation in fibromyalgia" in the "Non-
invasive brain stimulation lab" (NBS) at the university medicine Göttingen ... |
a99e0d957aed21a38449641e4acf1bd779197c5c2f4da4c7cf8222bf72bdb382 | Python | 1,393 | 15 | """Record literal URLs in built assets alongside the browser's request audit."""
import hashlib,json,re
from pathlib import Path
ROOT=Path(__file__).resolve().parents[2];dist=ROOT/'explorer/dist'
assets=[]
for p in sorted(dist.rglob('*')):
if p.is_file() and p.suffix in {'.js','.css','.html'}:
s=p.read_text();assert... |
e07fdee7c2c83fc8afa13ab1cd18b39ec34d5daca639c7361b9fb4d24a01bb04 | Python | 1,393 | 39 | import numpy as np
from rscvp.util.cli.cli_celltype import CellTypeSelectionOptions
from argclz import AbstractParser, as_argument
from neuralib.plot import plot_figure
__all__ = ['OverviewSessionStat']
class OverviewSessionStat(AbstractParser, CellTypeSelectionOptions):
DESCRIPTION = 'Compare fraction of varia... |
080524b1fde9ce01377553822a02f4c030e63760f7fd2d4f4680aaae957791e8 | Python | 1,394 | 42 | """Example code for plotting power maps calculated using the state/mode spectra
estimated from the source reconstructed data and inferred state/mode time course.
The spectra can be calculate with a multitaper (in the case of a state time
course) or regression (in the case of a mode time course).
See examples/spectra/... |
1d454baa19f3e2e7c532e8aa9f071107ea09e98f8be6a76e794e1493384a5ea5 | Python | 1,394 | 45 | from PyQt5 import QtGui, QtWidgets
from PyQt5.QtCore import Qt, QRect
class ModeToggle(QtWidgets.QPushButton):
def __init__(self):
super().__init__()
self.setCheckable(True)
self.setMinimumWidth(44)
self.setMinimumHeight(132)
def paintEvent(self, event):
if self.isChec... |
a2fff718eb85c82baf1318102719d54c8c69cafe6821d18e587e478aae282321 | Python | 1,394 | 49 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2023/6/3 15:23
# @Author : SONG-LE
# @知乎 : https://www.zhihu.com/people/xiao-xue-sheng-ye-xiang-xie-shu
import time
import numpy as np
import BoxCountingMethod_Solid
import Draw
import data_excel
import nibabel as nib
import os
# import r_tif
# Set the directory... |
4ad995b46c91fe66f9bccb9cdde4687f19796aaacbb0d2db75b5c4e1e8ff9cfd | Python | 1,395 | 54 | import argparse
from datetime import datetime
from deepreg.train import train
name = "grouped_mask_prostate_longitudinal"
# parser is used to simplify testing
# please run the script with --full flag to ensure non-testing mode
# for instance:
# python script.py --full
parser = argparse.ArgumentParser()
parser.add_ar... |
75803f1d9a3a4fc2f8628daad6d906b0b13c9b403a9baf607c71c8f1b1373d4b | Python | 1,395 | 53 | from __future__ import absolute_import
import warnings
from .market1501 import Market1501
from .msmt17 import MSMT17
from .personx import PersonX
from .veri import VeRi
from .dukemtmcreid import DukeMTMCreID
from .brain import Brain #RWM
from .brain_segs import Brain_Segs #RWM
__factory = {
'market1501': Marke... |
6e125a8cc180fb757e26463170404e499265ae7c24ebb9c81689347a26df12fb | Python | 1,396 | 52 | import sys
import os
import glob
from optparse import OptionParser
USAGE = """
write-mrsfast-ksearch-cmds.py --kdir <dir of kmer fasta files> --fa <fasta> --out <out file for cmds>
writes out cmds for mrsfast
"""
###############################################################################
parser = OptionParse... |
ea47fcfad205bf5168c2ce7e646f3d63d44b46b6e8523637176e50ddf18aba1d | Python | 1,396 | 31 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
import timm
import torch
from huggingface_hub import hf_hub_download
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_i... |
90123392610cdf0d561f9d00fc412bf5d570baf338ed1b07ea9a5c8884fc430e | Python | 1,397 | 29 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
f71a50f11955b47a04c08c949164291c9bc7e76f28e6e7c4672eaf7aef71c3b8 | Python | 1,397 | 59 | #!/usr/bin/env python
"""
Run HAL for testing Steve.
Hazen 11/18
"""
import os
import subprocess
import sys
import threading
import time
import traceback
from PyQt5 import QtWidgets
import storm_control.hal4000.hal4000 as hal4000
import storm_control.sc_library.hdebug as hdebug
import storm_control.sc_library.param... |
44c35869af8b3a66032aa3d72189792a8fce9aba83e3ebc656ddcc61d6e4a562 | Python | 1,398 | 41 | from copy import deepcopy
from unittest.mock import MagicMock
import numpy as np
from eir.data_load.data_preparation_modules import prepare_sequence
from eir.setup.schemas import SequenceInputDataConfig
def test_prepare_sequence_data():
test_input = np.array(list(range(100)))
test_input_copy = deepcopy(test... |
89104cd65f45c4f10c17498476becd28a0bd4b39ee2f713cd98e69292aa1b194 | Python | 1,398 | 56 | import numpy as np
import matplotlib.pyplot as plt
from parameters import *
def plot_raster_and_PSTH(times, sources, bin=30):
plt.figure(figsize=(60, 80))
plt.subplot(311)
plt.plot(times, sources, "|", color="k")
plt.ylim([100, 200])
plt.xlim(0, tfinal)
plt.ylabel("neuron ID")
plt.subplo... |
876901c2f19b229e6d45722c58859dc39d6d94f9e67d3805ed4e022f1c7bfc10 | Python | 1,399 | 47 | # Generated by Django 3.2.16 on 2022-11-30 08:44
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("engine", "0060_alter_label_parent"),
]
operations = [
migrations.AlterField(
model_name="labeledshape",
name="type"... |
2b3b748f97ee7ff2a3640f3ef95d90cd337d759bdd5c14da3e8d93410c95a55e | Python | 1,400 | 60 | import os
import uuid
from unittest import TestCase
from unittest.mock import ANY
import kb_python.stats as stats
from tests.mixins import TestMixin
class TestStats(TestMixin, TestCase):
def test_start(self):
s = stats.Stats()
s.start()
self.assertIsNotNone(s.start_time)
self.as... |
bc08053bea2c17541c787e898f2aed74482d05f5e73b1068eb6a75b83ad937bc | Python | 1,400 | 51 | from ..qt import *
import bisect
from ..config import ObservableCollection
import typing
import functools
class IntanWidget(QWidget):
def __init__(self, node, stub):
super().__init__()
if 'Channels' not in node:
node['Channels'] = []
channels = node['Channels']
layout = QVBoxLayout()
qlis... |
f159608baead5610724e21f76cc8a628bef66277726691f822e7a80b7e664226 | Python | 1,400 | 49 | # -*- coding: utf-8 -*-
"""
Created on Fri Mar 31 11:12:54 2023
@author: axthi
"""
import sys
# --------------------------------------------------
# NOTE: Update this path to fit to your installation
path_to_utils = 'C:/Users/axthi/simnibsN/memoslap_utils/'
sys.path.append(path_to_utils)
import simnibs_memoslap_util... |
ff117e9451aae161d457cb4f5a558b3908a01e610d95c5ea216727538cc8290f | Python | 1,400 | 37 | # -*- coding: utf-8 -*-
#
# test_event_generators.py
import unittest
import arbor as arb
from arbor import units as U
"""
all tests for event generators (regular, explicit, poisson)
"""
class TestEventGenerator(unittest.TestCase):
def test_event_generator_regular_schedule(self):
cm = arb.cell_local_lab... |
b869a94dd1638206dfacb9574709e15c5dca706edb5bd8bda6a6d8eaa5b55136 | Python | 1,402 | 51 | from __future__ import annotations
from pathlib import Path
from typing import Final
import pytest
from PySide6.QtWidgets import QMessageBox
from pytestqt.qtbot import QtBot
from ..conftest import close_or_pause
from .conftest import MainWinFactory
from .conftest import show_window_and_wait_for_imagedata
@pytest.m... |
d2b3081cba1b9b3f1c078430d7f04b127550398b8f72831178e045c818962387 | Python | 1,402 | 52 | # Copyright (c) DP Technology.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import lmdb
import os
import pickle
import torch
import numpy as np
import collections
from functools import lru_cache
from . import data_utils
import logging
logge... |
461244a181abe1398d85cb4763372007b4ecdfa7cd9b6eec62879190d4950e9d | Python | 1,403 | 37 | # encoding=utf-8
from __future__ import unicode_literals
from whoosh.analysis import RegexAnalyzer, LowercaseFilter, StopFilter, StemFilter
from whoosh.analysis import Tokenizer, Token
from whoosh.lang.porter import stem
import jieba
import re
STOP_WORDS = frozenset(('a', 'an', 'and', 'are', 'as', 'at', 'be', 'by', '... |
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