sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
716b59aa0356fb521703ab1a9d8167b1f48f94c2e4a3d97c4c3ad529ac77123d | Python | 473 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['alexnet_7be5be79'] = lambda: ModelCommitment(identifier='alexnet_7be5be79',
... |
737a4e2a70490e374c3a77ecbd6772c95315d479fd98b8cfd837e8637293e7a0 | Python | 473 | 17 | # Script to copy the saved state from the folder with the newest timestamp
# (c) Jannik Luboeinski 2021
import numpy as np
from pathlib import Path
import shutil
import os
rawpaths = Path('.')
folders = sorted([str(x) for x in rawpaths.iterdir() if x.is_dir() and "_TRIPLET" in str(x)])
latest_folder = folders[len(fol... |
dd3a02b8a10f290bb18777023950d2a3e6b78b01d1b06938f46807ef02fc7f9f | Python | 473 | 17 | import torch
from .base_reducer import BaseReducer
class MeanReducer(BaseReducer):
def element_reduction(self, losses, *_):
return torch.mean(losses)
def pos_pair_reduction(self, losses, *args):
return self.element_reduction(losses, *args)
def neg_pair_reduction(self, losses, *args):
... |
1a44cac76817a96ab607d0fa0494fbd8a0aab4940ec02b82cf27c5d477b09d00 | Python | 474 | 18 | BATCHGLM_OPTIM_GD = False
BATCHGLM_OPTIM_ADAM = False
BATCHGLM_OPTIM_ADAGRAD = False
BATCHGLM_OPTIM_RMSPROP = False
BATCHGLM_OPTIM_NEWTON = False
BATCHGLM_OPTIM_NEWTON_TR = False
BATCHGLM_OPTIM_IRLS = False
BATCHGLM_OPTIM_IRLS_GD = False
BATCHGLM_OPTIM_IRLS_TR = True
BATCHGLM_OPTIM_IRLS_GD_TR = True
BATCHGLM_PROVIDE_B... |
57858ca086379b64cf1dc3369ea993a9cb3d8339832e76f7bbc227f714924436 | Python | 474 | 20 | import os
import numpy as np
import warnings
def preprocess_vol(vol):
assert vol.ndim == 4, f"Expected 4D image, got {vol.ndim}D"
if vol.shape[1] != 4:
warnings.warn(
f"Expected 4 channels, got {vol.shape[1]} channels. "
"This may lead to unexpected behavior."
)
# C... |
960e8b498183f397f7618b4444c841a22307b354a4dcdf2a1b48c7161fe4a7fd | Python | 474 | 13 | import setuptools
setuptools.setup(
name="biographs",
version="0.1",
author="Rodrigo Dorantes-Gilardi",
author_email="rodgdor@gmail.com",
description="A package to work with protein structure networks",
url="https://github.com/rodogi/biographs",
keywords=["protein contact network", "protein... |
80a3b23b6e41b2fcd83557c6d449f09214bb92b79f12c5ecf40684e6a7067591 | Python | 475 | 5 | """CoRelAy is a package to compose small-scale (single-machine) analysis pipelines. Pipelines are designed with a number of steps
(:py:class:`~corelay.pipeline.base.Task`) with default operations (:py:class:`~corelay.processor.base.Processor`). Any step of the pipeline may then
be individually changed by assigning a ne... |
9917fb256a889b91f3dcb508c96031dfa5ae452054b3a9bc2a41fa871a6aabb1 | Python | 475 | 18 | #!/bin/env python
import numpy as np
import math
import sys
inp = sys.argv[1]
lines = np.loadtxt(inp, dtype=np.float, comments='#', usecols=(0,1,2,3), unpack=False)
nlines = len(lines)
for i in range(nlines):
for j in range(i+1, nlines):
x0, y0, z0, d0 = lines[i]
x1, y1, z1, d1 = lines[j]
# dist = math... |
a3fa5ff71e2e2eca8cf853b7c10c4a6f9a433d3d8bcc5ce07b97dab6905c1d06 | Python | 475 | 18 | # Copyright (c) OpenMMLab. All rights reserved.
from mmcv.utils import collect_env as collect_base_env
from mmcv.utils import get_git_hash
import depth
def collect_env():
"""Collect the information of the running environments."""
env_info = collect_base_env()
env_info['Depth'] = f'{depth.__version__}+{ge... |
f6b4ef8985dca7d396132db6fac5e912dc1f93ca884499042cd1cd832c0a2b7a | Python | 476 | 12 | from brainsmash.workbench.geo import volume
from brainsmash.mapgen.sampled import Sampled
import scipy.io as sio
coord_file = "voxel_coordinatesageType10NgE.nii.txt"
output_dir = "../0~8"
filenames = volume(coord_file, output_dir)
brain_map = "valueforsp.nii.txt"
gen = Sampled(x=brain_map, D=filenames['D'], ... |
30f5cde9b3981a0e6642db856c279620a19e2a9a4f69fe65331a4d96ed0a3800 | Python | 477 | 13 | from generate_features import account
import json
import numpy as np
dataset_name='Twibot-22'
#dataset_path='/data2/whr/czl/TwiBot22-baselines/datasets'+'/'+dataset_name
files=['train','test']
for file in files:
with open(dataset_name+'/' + file + '.json','r') as f:
data=json.load(f)
acc_mat=account... |
822c86a5d60f27ae3fabfc4b8589184702f54ce6a7dc3c893b8f7b5f546e0ec8 | Python | 477 | 8 | from brainscore_vision import model_registry
from .helpers.helpers import CORnetCommitment, _build_time_mappings
from .model import get_model, get_layers, TIME_MAPPINGS
model_registry['CORnet-S'] = lambda: CORnetCommitment(identifier='CORnet-S', activations_model=get_model('CORnet-S'),
... |
d6fd04f229d85f779cb8aad24f5fcefdb47e2e34abeda901b69e6c545081fc4f | Python | 477 | 15 | """
A simple subclass of PlotWidget to add a lasagna viewbox in Qt Designer
"""
from pyqtgraph import PlotWidget
from lasagna.lasagna_viewBox import lasagna_viewBox
class LasagnaPlotWidget(PlotWidget):
def __init__(self, *args, **kwargs):
if 'viewBox' not in kwargs.keys():
kwargs['viewBox'] =... |
f029d18d75e0dd04a16c2ea37778f9545a11e0a48642c082692b35af46d23008 | Python | 477 | 11 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['dinov2_vitl14_reg_lc_featread'] = lambda: ModelCommitment(
identifier='dinov2_vitl14_reg_lc_featread',
activations_model=get_mod... |
196a43062d76da2e7371f24812e19c50227b874cbbd0e6b6ce460ac6b559e514 | Python | 478 | 20 | from rscvp.spatial.main_slb import PositionLowerBoundOptions
from rscvp.util.util_demo import run_demo
class ExampleRun(PositionLowerBoundOptions):
exp_date = '210315'
animal_id = 'YW006'
plane_index = 0
neuron_id = 0
session = 'light'
shuffle_times = 300
with_heatmap = True
signal_typ... |
575824940ae9a1b127bbf2a7b72501f0c74332937b767d426dba33cfd520e5f8 | Python | 479 | 21 | """Print the free energy of different runs.
"""
import pickle
import numpy as np
best_fe = np.inf
for i in range(1, 11):
try:
history = pickle.load(open(f"results/run{i:02d}/model/history.pkl", "rb"))
free_energy = history["free_energy"]
print(f"run {i}: {free_energy}")
if free_en... |
ad0a623c1d632f994f80624b9c66beb98bc3118e1284c73fdfad4116c91f0fcf | Python | 479 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['efficientnet_b0'] = lambda: ModelCommitment(identifier='efficientnet_b0',
... |
c080e6f48e55a64519304496ec9f92011b7df8c1b0538a14bece33913b4e54d5 | Python | 481 | 15 | from neuralib.util.utils import ensure_dir
from rscvp.atlas.main_roi_top_view import RoiTopViewOptions
from rscvp.util.io import RSCVP_CACHE_DIRECTORY
from rscvp.util.util_demo import run_demo
class ExampleRun(RoiTopViewOptions):
SOURCE_ROOT = ensure_dir(RSCVP_CACHE_DIRECTORY) / 'rscvp_dataset' / 'analysis' / 'hi... |
ffa6883864c168e866126000f562fa8690a890e00e217cce8d0680505cb5d164 | Python | 481 | 16 | from setuptools import setup, find_packages
import pathlib
here = pathlib.Path(__file__).parent.resolve()
setup(
name="bannotator",
version="0.1.0",
author="Xingjian Zhang",
description="A GUI application to annotator animal behavior videos",
packages=find_packages(),
project_urls={"Source Co... |
8622e3fc86d980ab7e94edf29b313d35c6e3eea583124dc9334ca53d7e968a2d | Python | 482 | 20 | """# Directory dialog widget
A dialog to select a directory.
"""
from pathlib import Path
from magicgui import magicgui
# Select a directory, instead of file(s)
@magicgui(directory={"mode": "d", "label": "Choose a directory"})
def directorypicker(directory=Path("~")):
"""Take a directory name and do something ... |
cac90496eb2a5053045c0c11b3cb0006c992a88740e94f9715c42a12ec5d858c | Python | 482 | 6 | from mmsdk.mmdatasdk.computational_sequence.computational_sequence import computational_sequence as computational_sequence
from mmsdk.mmdatasdk.dataset.dataset import mmdataset as mmdataset
from mmsdk.mmdatasdk.dataset.standard_datasets import CMU_MOSEI as cmu_mosei
from mmsdk.mmdatasdk.dataset.standard_datasets import... |
fb5b5f617071a5bfb2dab601ec7e680f64746f16f011f297211773f1dcd6e492 | Python | 482 | 19 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from .bot_sort import BOTSORT
from .byte_tracker import BYTETracker
from .deep_oc_sort import DeepOCSORT
from .fast_tracker import FASTTracker
from .oc_sort import OCSORT
from .track import register_tracker
from .track_tracker import TRACKTRACK
__all... |
9cb74ad5ccf6d881006f269f9613983971bd5ea0577e6c8f2d5836e06578d460 | Python | 483 | 18 | #!/usr/bin/env python
"""
Test getting the stage position.
"""
from storm_control.test.hal.standardHalTest import halTest
def test_hal_gsp_1():
halTest(config_xml = "none_tcp_config.xml",
class_name = "GetStagePosition1",
test_module = "storm_control.test.hal.tcp_tests")
def test_hal_gsp... |
44274c75f6d9ea1cca3c02df8b1cd0e7916440106eeaa3fc6d0a340105f91b34 | Python | 484 | 5 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['deit3_base_patch16_224_fb_in1k_gram_aligned_dinov3'] = lambda: ModelCommitment(identifier='deit3_base_patch16_224_fb_in1k_gram_aligned_d... |
5aa1b824c017241503f4f37806b5d9e78c3890d55230cdb50d99b3592e1353e1 | Python | 484 | 11 | """Vendored numeric helpers for iterative 2D background fitting.
Currently holds the 1D per-sector cone-background model used by the step-0
projection pass. Copied from the bg-optimization research repo
(``src/bg_removal/gen_bg_fit/fit_sector_var_model.py``); depends only on
numpy/scipy so it is self-contained.
"""
f... |
9a5ea4e76a057f5fa5a03b9f1bc09c7ca3cc7ce58ba04864c1d05ca08ea84138 | Python | 484 | 13 | from self_attention_cv import UNETR
import torchinfo
if __name__ == '__main__':
model = UNETR(img_shape=(32, 256, 256), input_dim=1, output_dim=2,
embed_dim=512, patch_size=16, num_heads=10,
ext_layers=[3, 6, 9, 12], norm='instance',
base_filters=16,
... |
a1e4fa8d5117f2aee6c5cc083b3eba2d64551a8b26e9a9f05ca773fa27d3b58c | Python | 484 | 5 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['convnext_base_fb_in22k_ft_in1k_gram_aligned_dinov3'] = lambda: ModelCommitment(identifier='convnext_base_fb_in22k_ft_in1k_gram_aligned_d... |
e16005b2186812049719532406e846e649f563d21db1d36d0bdfd3638f31a9a1 | Python | 484 | 17 | import argparse
import os
parser = argparse.ArgumentParser()
parser.add_argument('dataset', type=str, help='name of the dataset used for training')
args = parser.parse_args()
print('running DeeBotPro on '+args.dataset)
order="python "+args.dataset+".py"
os.system(order)
print('process_1 finished')
order="python des_em... |
e39ffaa52926b4008a0f34e9bffeae34edac3c4c095510755656661ddd49dece | Python | 484 | 24 | #!/usr/bin/env python3
"""
command line tool to convert voxel coordinates to world coordinates
usage: voxel-to-world.py <nifti_file> <x> <y> <z>
"""
import sys
import nibabel as nib
if len(sys.argv) != 5:
print("Usage: voxel-to-world.py <nifti_file> <x> <y> <z>")
sys.exit(1)
nifti_file = sys.argv[1]
x = in... |
0a8114e6e49ffc39a07422aedc03180ecc114db95aae4060c0f9d647dd541d81 | Python | 485 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['antialias-resnet152'] = lambda: ModelCommitment(identifier='antialias-resnet152',
... |
2d77efdfeb252d6d350bba496f16ce072f0bb1539e07845598e2f63973227fb1 | Python | 485 | 24 | import requests
def send_request(url: str, payload: list[dict]):
response = requests.post(url, json=payload)
return response.json()
payload = [
{
"flchain": {
"age": 65,
"sex": "M",
"flcgrp": "1",
"kappa": 1.5,
"lambdaport": 1.2,
... |
8462215e5bb1d370076c6d2ca2f9665dd15162cadb8a720cf04ade14d2d5f807 | Python | 485 | 12 | from .l1_ngc_da_bnac import L1_NGC_DA_bNAC
from .l23_pc_cadpyr import L23_PC_cADpyr
from .l4_lbc_cacint import L4_LBC_cACint
from .l4_lbc_cstut import L4_LBC_cSTUT
from .l4_lbc_dnac import L4_LBC_dNAC
from .l4_nbc_cacint import L4_NBC_cACint
from .l4_nbc_dnac import L4_NBC_dNAC
from .l4_sbc_bnac import L4_SBC_bNAC
from... |
ce3abae88b2035a5e1f90c0bd5a6fa22297ef7fd8af1d066fc2d337163dae2c0 | Python | 485 | 23 | #!/usr/bin/env python3
import argparse
import os
import sys
import arbor
P = argparse.ArgumentParser(
description="Verify that a mechanism catalogue can be loaded through Python interface."
)
P.add_argument("catname", metavar="FILE", help="path of the catalogue to test.")
args = P.parse_args()
catname = args.ca... |
4c73ab111e3e77e5b4d94ff58600a081bc785c7e82ce834337b8ceea0aa78dff | Python | 486 | 14 | import os
import subprocess
# List of .ui files to convert and merge
path_to_ui = os.path.join(os.getcwd(), "bannotator","ui")
ui_files = [f for f in os.listdir(path_to_ui) if f.endswith(".ui")]
# Convert .ui files to .py files
for ui_file in ui_files:
py_file_path = os.path.join(path_to_ui,'ui_'+ ui_file.replac... |
fb86bcdb6fc29a89c45f66800753f062bc1520f8c169eeee7350aceadefbe1fb | Python | 486 | 8 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['ViT_L_32_imagenet1k'] = lambda: ModelCommitment(identifier='ViT_L_32_imagenet1k',
... |
45d6560af775b38ccc2d93501e741d7854cede7c084cb91e5e375eb22f4609e1 | Python | 487 | 19 | #read_dataset_by_folder.py
#reads a dataset from a dataset folder
import mmsdk
from mmsdk import mmdatasdk
import argparse
parser = argparse.ArgumentParser(description='Reading dataset from a folder')
parser.add_argument('path', metavar='path', type=str,
help='the folder path to read dataset fro... |
65301dc89a7f214cb4ad4dc88bf1f14fe26e5700e0b1ac1424a5c6a3011bcca2 | Python | 487 | 21 | import os
import subprocess
import unittest
import pytest
SVMTK_test = os.path.abspath(
os.path.join(os.path.dirname(__file__), "bin", "SVMTK_test")
)
class MainTest(unittest.TestCase):
@pytest.mark.skipif(not os.path.exists(SVMTK_test), reason="C++ tests not built")
def test_cpp(self):
print("\... |
9ce11508e49e2390fbaee599153473787eb267f7a1bae07c91d1afd175722bda | Python | 487 | 16 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
from .build_sam import (
build_sam,
build_sam_vit_h,
build_sam_vit_l,
build_sam_vit_b,
sam_model_regis... |
9d088b56d292da8e762fe3c2b7f653d98ee6dff78c50373746504b1565191473 | Python | 487 | 17 | import os
import random
import numpy as np
import torch
def setup_seed(seed):
"""Set random seed for reproducibility across all libraries."""
torch.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
np.random.seed(seed)
random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
os.environ[... |
b94812281730efe9f0205c48e67852ecea6f05138a6fa9658d32bdc6e9627209 | Python | 487 | 13 | from brainscore_vision import metric_registry
from .metric import ErrorConsistency
metric_registry['error_consistency'] = ErrorConsistency
BIBTEX = """@article{geirhos2020beyond,
title={Beyond accuracy: quantifying trial-by-trial behaviour of CNNs and humans by measuring error consistency},
author={Geirhos, Rober... |
cf6647ee9ec4c1838c3307a1c8317b5a348951bc2bff89a2bf1cc9a5fc3a3790 | Python | 487 | 19 | def unique_keep_order(lst: list):
""" Get all unique elements from a list without altering the order in which
the elements appear. Note that set() does alter the order, which can cause
problems in some parts of the code.
Params
------
lst: list with arbitrary data
Returns
-------
l... |
fc5a7def02c8d5cc45148d5094e92f5882b0766b5068f1201fdeca9ad4036682 | Python | 487 | 17 | from abc import abstractmethod
class Reader:
def __init__(self):
pass
@abstractmethod
def _filename(self, index, basename=False, absolute=False):
pass
def filename(self, index, basename=False, absolute=False):
return self._filename(index, basename=basename, absolute=absolute)... |
1f9d83eea17cc15be2748dc8259a02bcf917650c2cc5a3e0f51fbc4d35ffc9a4 | Python | 488 | 21 | # coding=utf-8
"""
Tests for deepreg/model/backbone/interface.py
"""
import deepreg.model.backbone as backbone
def test_backbone_interface():
"""Test the get_config of the interface"""
config = dict(
image_size=(5, 5, 5),
out_channels=3,
num_channel_initial=4,
out_kernel_initi... |
3dc14aeaf0c2062797816aa1ec1d6d30c7d1fbdcd5a821eddecb6527b16d752f | Python | 488 | 23 | from mpi4py import MPI
world = MPI.COMM_WORLD
color = None
leader = None
if world.rank == 0:
color = 0
leader = 1
else:
color = 1
leader = 0
group = world.Split(color)
inter = group.Create_intercomm(0, world, leader, 42)
if __name__ == "__main__":
print(f"{world.rank:2d}/{world.size:2d} {group.r... |
7d9f67b55dff8b07df8977e64c0c7bd478d6ef340b2be696f14121328851e7dc | Python | 488 | 16 | #!/usr/bin/env python
"""DEPRECATED shim -> `morphometrics pycurv`.
This script has moved into the installable `surface_morphometrics` package and is
now invoked as `morphometrics pycurv ...`. This thin wrapper forwards to that
command and will be removed in a future release.
"""
import sys
from surface_morphometrics... |
aee63b80b62a749f33f89eb95ec8feac5bb35367017d9a09a9275839ff4f3a61 | Python | 488 | 25 | from setuptools import setup, find_packages
setup(
name='Lasagna',
version='0.1',
packages=find_packages(),
include_package_data=True,
install_requires=[
'pyqt5==5.15.6',
'numpy',
'tifffile',
'pynrrd',
'pyqtgraph',
'pyyaml',
'sip',
'sc... |
bb1f827787a7e5c8af000ba1b768e72349ba8e1cef7694aeb763878c587d0fd0 | Python | 488 | 23 | from scipy import stats
import numpy as np
from .base import Distribution
class HalfNormal(Distribution):
"""HalfNormal prior.
Parameters
----------
sigma : scalar or ndarray
Standard deviation of distribution
"""
def __init__(self, sd):
self._sd = np.asarray(sd)
... |
eee8c623a81eb25296f9792d8927f23771e8a3d9bbd26d15b38da84ec166236c | Python | 488 | 15 | def check_and_add_suffix(filename: str, suffix: str) -> str:
"""
Adds a suffix to the filename if it doesn't already have it.
Parameters:
filename (str): The filename to check and potentially modify.
suffix (str): The suffix to add to the filename.
Returns:
str: The filename wi... |
13bd7f7018c67f964361cfd7d9646d41ae448ee927a2f147b5f16505362c49e1 | Python | 489 | 26 | #
# A very simple test of Kilroy.
#
from PyQt5 import QtCore
import time
import pytestqt
import storm_control.sc_library.parameters as params
import storm_control.test as test
import storm_control.fluidics.kilroy as kilroy
def test_kilroy_starts(qtbot):
parameters = params.parameters(test.kilroyXmlFilePathAnd... |
75e26651172d626f29525f306ecd71e44d0fafdd1432eb252228705f8291a726 | Python | 489 | 18 | import pandas as pd
label = pd.read_csv('/data2/whr/czl/TwiBot22-baselines/datasets/cresci-2017/label.csv')
main_user = pd.read_csv('./user_feature.csv')
user = main_user.loc[0:len(main_user)-1]
user_list = list(user['user_id'])
del_list = []
for i,r in label.iterrows():
if r[0] not in user_list:
del_li... |
7d96d2528446476b5d7afea3fb3e5697c11dbd0b1983775e47c1fdf91a539f56 | Python | 489 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['mobilenet_v2_1_4_224'] = lambda: ModelCommitment(identifier='mobilenet_v2_1_4_224',
... |
9071411a45364894dcda20747f6f0718584653fd1f53fdaf3b7144347c281284 | Python | 489 | 18 | class Loop:
"""
Class that stores a single for loop's information.
"""
def __init__(self, dimension: str, size: int, type: str = "temporal"):
"""
Initialize the loop with the given dimension string and size.
"""
self.dimension = dimension
self.size = size
... |
ddf6c4f8eabc3de79d951ea88cfaa5d4f757a79c102aabfd7adbbe91e821ca03 | Python | 490 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['mobilenet_v2_1_0_224'] = lambda: ModelCommitment(identifier='mobilenet_v2_1_0_224',
... |
ebe707947d464468cb2ff2517fa3c9f633d70b71a3ac03d7200f1ef48204944c | Python | 490 | 14 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from .version import version as __version__ # noqa
from .data import Alphabet, BatchConverter, FastaBatchedDataset # noqa
from .model impor... |
beff6e39e4c08400ec221158e91fac4329a68cdd5518f5d0b4803a98c089fbc1 | Python | 491 | 7 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['fixres_resnext101_32x48d_wsl'] = lambda: ModelCommitment(identifier='fixres_resnext101_32x48d_wsl',
... |
0e7f61a7a1dd8ed53c3be4d47dc5ab9ba502fb377492a65ecec48840f113ad40 | Python | 492 | 19 | import nilearn
import glob
from nilearn.image import threshold_img
import nibabel as nb
folder = '/Users/sebastiandresbach/data/s1Anfunco/Nifti/derivatives/sub-07/func/statMaps'
statMaps = sorted(glob.glob(f'{folder}/sub-07_D*vsAll_VASO.nii.gz'))
for i, statMap in enumerate(statMaps, start=2):
nii = nb.load(statM... |
12d632c78e73590fe201e589fb69ac8d0e5f2d70084b6ed088a3a309327ecdd5 | Python | 492 | 19 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from .common import Target
from .project_dataset import ProjectVisionDataset
from .task_dataset import TaskVisionDataset
from .transforms import (
ExtractBoundingBoxes,
ExtractInstanceMasks,
ExtractSingleLabelIndex,
LabeledBoxes,
... |
5af7ee3dda90ca98de553652e96d341b91d40c4c9bbf58b6316e244dd289f0b2 | Python | 492 | 13 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['eicircuit_resnet18_bn_20260919'] = lambda: ModelCommitment(
identifier='eicircuit_resnet18_bn_20260919',
activations_model=get... |
aa4758a74e06ae56c67837be449693d986cf72c179a8eab7a21c6ceffdb63ea4 | Python | 492 | 16 | #!/usr/bin/env python
"""DEPRECATED shim -> `morphometrics hist2d`.
This script has moved into the installable `surface_morphometrics` package and is
now invoked as `morphometrics hist2d ...`. This thin wrapper forwards to that
command and will be removed in a future release.
"""
import sys
from surface_morphometrics... |
efb059bc8dfc38015655860f7aee7b3fdc2417099253b11d606af0d9c2a49ace | Python | 493 | 25 | import pytest
try:
import fury # noqa: F401
from AFQ.viz.utils import Viz
test_viz = True
except ImportError:
test_viz = False
@pytest.mark.skipif(
not test_viz, reason="Skipping viz tests, unable to import viz utils"
)
def test_viz_name_errors():
Viz("fury")
with pytest.raises(
... |
f7e72de7013bc43f66240b445254a0b26d2f0adbf5536205d77c877f181794b8 | Python | 493 | 14 | from dtiplayground.dmri.common.tools.base import ExternalToolWrapper
class DTIEstim(ExternalToolWrapper):
def __init__(self,binary_path= None, **kwargs):
super().__init__(binary_path, **kwargs)
def estimate(self,dwi_path, output_path, options=[]):
arguments=[]
arguments+=['--dwi_image'... |
fcfa55a1e1cb61e9705ba953f1748f20cdbc0e9c70ee8f1adcebd19b2b3823b5 | Python | 493 | 16 | #!/usr/bin/env python
"""DEPRECATED shim -> `morphometrics stats`.
This script has moved into the installable `surface_morphometrics` package and is
now invoked as `morphometrics stats ...`. This thin wrapper forwards to that
command and will be removed in a future release.
"""
import sys
from surface_morphometrics.c... |
93bf17e432b9c45b55f9079b5c3fc36a2c9bf318c75802105393aea1fbf3bfa7 | Python | 494 | 11 | from brainscore_vision import stimulus_set_registry
from brainscore_core.supported_data_standards.brainio.s3 import load_stimulus_set_from_s3
# stimulus set
stimulus_set_registry['ImageNetSlim15000'] = lambda: load_stimulus_set_from_s3(
identifier="ImageNetSlim15000",
bucket="brainscore-storage/brainio-brainsc... |
ff341ece8867386564c04d016f915f3ea76d275197558e3f0617cd544cbacc69 | Python | 494 | 15 | import os
import numpy as np
# Data from Ahlgren et al 2016 NMRinBiomed
Delta = 7.5e-3 # 7.5 ms
delta = 7.3e-3 # 7.3 ms
# For DDE sequence we have
# b = 2y^2G^2d^2(D-d/3), c = 2yGdD => c = sqrt(b 2D^2/(D-d/3))
bval_file = os.path.join(os.path.dirname(__file__),'ballistic.bval')
b = np.loadtxt(bval_file)
c = np.sqrt(b... |
1a39933b71438d4a35909abae27482077ff395a17029365a5ccff52fd60c9cde | Python | 495 | 19 | # -*- coding: utf-8 -*-
# @Author : LG
from .transforms import ResizeLongestSide
import numpy as np
from typing import Tuple
import cv2
class Med2dTransforms(ResizeLongestSide):
def apply_image(self, image: np.ndarray):
image = cv2.resize(image, (256, 256), interpolation=cv2.INTER_NEAREST)
ret... |
264667f099d51b3f0aff8da6d1e8feecdda386f615e1d88d8c39d0bae3318f2b | Python | 495 | 16 | """
Batch_Location Decoder
"""
import re
import numpy as np
from pathlib import Path
from LocationDecoder import LocationDecoder
FolderLocation = Path(r'D:\Data\Lobster\Lobster_Recording-200319-161008\20JUN1')
OutputFileLocation = Path(r'D:\Output')
for tank in FolderLocation.glob('#*'):
tank_name = re.search('#.... |
465ece07aff0651854a5932ba3e4ad52265f13396008ab647ba491d4f45bfd89 | Python | 495 | 27 | # Default predictor settings
DEFAULT_KRR_SETTINGS = {
"alpha": 1.0,
"kernel": "linear",
"gamma": "",
"degree": 3,
"coef0": 1.0,
}
DEFAULT_MLP_SETTINGS = {
"network": {
"hidden_layers": [24, 12, 6],
"activation_fn": "ReLU",
},
"optimization": {
"optimizer": "Adam... |
57dcdb3cb95086c5a638cb174c5614b46132cc6c99f3126984078ff1ee631992 | Python | 495 | 9 | from reducers.avg_non_zero_reducer import AvgNonZeroReducer
from reducers.base_reducer import BaseReducer
from reducers.class_weighted_reducer import ClassWeightedReducer
from reducers.divisor_reducer import DivisorReducer
from reducers.do_nothing_reducer import DoNothingReducer
from reducers.mean_reducer import MeanRe... |
9048ad7cd64fc5cd74d91ca43d0025bc564c9ec6c2aaf1ae1c803082930f3238 | Python | 495 | 13 | import numpy as np
# filename = str(baseline_atp) + '_regular_'+str(int(firing_freq))+'Hz_' + str(t_ca[ii]) + '_' + labels[ii] + '.npz'
c_reg_fn = '100_regular_20Hz_7_Control.npz'
l_reg_fn = '100_regular_20Hz_20_Letm1.npz'
c_reg = np.load(c_reg_fn)
l_reg = np.load(l_reg_fn)
np.savetxt('Control_Ca_20Hz.csv',
... |
936bedcd6bd976251663134735535d379dafdaa4d0cb574ae8b82ec50de11cac | Python | 495 | 20 | """# Password login
A password login field widget.
"""
from magicgui import magicgui
# note that "password" is a special keyword argument
# it will create a password field in the gui by default
# (unless you override "widget_type")
# whereas "password2" will be a normal text field
# (unless you override "widget_typ... |
51ccbb3148341540bcfe391d60e59fb132301c34413be8b882dd8cb55a951c1a | Python | 496 | 20 | import pyro # type: ignore
DEFAULT = dict(
num_epochs=5000,
optimizer=pyro.optim.ClippedAdam,
optimizer_kwargs={"lr": 0.01, "betas": (0.95, 0.999)},
scheduler=None,
loss=pyro.infer.TraceMeanField_ELBO,
loss_kwargs={"num_particles": 1},
)
TEST = dict(
num_epochs=200,
optimizer=pyro.op... |
70c14f46f04cdc9800896190ad26f0aced73112f3a747eb649018f8e6c7caa90 | Python | 497 | 19 | import unittest
from ogo.cli.ImageExam import ImageExam
class Test_ImageExam(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tests, if... |
9c33950243f286243ec2f11178cd93f59bb758b5f0df43cd60f0f3643181284b | Python | 497 | 23 | from __future__ import absolute_import
class AverageMeter(object):
"""Computes and stores the average and current value"""
def __init__(self):
self.val = 0
self.avg = 0
self.sum = 0
self.count = 0
def reset(self):
self.val = 0
self.avg = 0
self.sum... |
9dd3403b196870546f8d3c6618e7a3b4b9c2880c2333ab426be3c725806827e3 | Python | 497 | 19 | """
Functions parsing the config optimizer options
"""
import tensorflow as tf
def build_optimizer(optimizer_config: dict) -> tf.optimizers.Optimizer:
"""
Parsing the optimiser options and parameters
from config dictionary.
:param optimizer_config: has key name and other required arguments
:retu... |
d759a17bd3513ab056ae5dfec8ab9b362852b53ed30dbd5fd6808fa881b6a5f1 | Python | 497 | 26 | """
nelpy auxiliary objects
``nelpy`` is a neuroelectrophysiology object model and data analysis
suite.
"""
from ._results import ResultsContainer, load_pkl, save_pkl
from ._session import Session
from ._tuningcurve import (
DirectionalTuningCurve1D,
TuningCurve1D,
TuningCurve2D,
TuningCurveND,
)
__a... |
3af2170672fe72aa91b59582f5b1035ee8c94a982f86e524f31859ce02f9a616 | Python | 498 | 20 | # Generated by Django 4.2.18 on 2025-03-12 18:20
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("quality_control", "0007_project_quality"),
]
operations = [
migrations.AddField(
model_name="qualitysettings",
name... |
476c811c7523b831aab9f064b8cba06608751b4f0c7d3167209e022d8a04328b | Python | 498 | 9 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_model, get_layers
model_registry['cvt_cvt-w24-384-in22k_finetuned-in1k_4'] = \
lambda: ModelCommitment(identifier='cvt_cvt-w24-384-in22k_finetuned-in1k_4',
... |
83b38d24157afc43f6645792d0573629458535445a7845359f403bbb906bee36 | Python | 498 | 14 | from pathlib import Path
import yaml
from deep_events.database import reconstruct_from_folder, get_collection
FILEPATH = Path(__file__).parents[1]
with open(FILEPATH / "test_database/settings.yaml", "r") as stream:
COLLECTION = yaml.safe_load(stream)["COLLECTION"]
def test_reconstruct():
folder = FILEPATH / "... |
2208b76f01e1b31755b6e2ad186ad6e2acc6440c9ad46eb416681245c65cb691 | Python | 499 | 19 | import unittest
from ogo.util.write_txt import write_txt
class Test_Write_TXT(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tests, i... |
5aebcc012a4ce50495130b3a1db0c94a5e6f842dec36ce9e56916b823b8911a9 | Python | 499 | 19 | import unittest
from ogo.util.write_csv import write_csv
class Test_Write_CSV(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tests, i... |
838deb470f8bb9965223431fccccc7120c0465f8f5f2ba7d186ab6c57df86765 | Python | 499 | 18 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from abc import ABCMeta, abstractmethod
from attrs import define, field, validators
from redis import Redis
@define
class BaseMigration(metaclass=ABCMeta):
name: str = field(validator=[validators.instance_of(str)])
app_label: str = field(v... |
a1bf531b38cf1f3c850fe0afe7a38fb398b0b8c5a3157286bf2defa1f3e365b7 | Python | 499 | 19 | import warnings
warnings.filterwarnings("ignore", message="It is not recommended to directly access")
import numpy as np
import torch
import secrets
import random
def generate_random_seed():
return secrets.randbelow(2 ** 32)
def set_seed(seed):
print(f"[INFO] Using random seed: {seed}")
random.seed(seed)... |
a9f1dc8e9a2433dced52d6712fae3ff6926cadeb5c398409fc62ed20d08d6ade | Python | 499 | 14 | from argclz.commands import parse_command_args
from .main_cache_bayes import BayesDecodeCacheBuilder
from .main_decode_analysis import DecodeAnalysisOptions
from .main_disengagement import DecodeDisengageOptions
parse_command_args(
usage='python -m rscvp.model CMD ...',
description='do the related analysis for... |
d186365ce680e48de2e93023a8a061a428a27f78e6de02736f200639ea13623f | Python | 499 | 17 | from pathlib import Path
tree_str = ''
def generate_tree(pathname, n=0):
global tree_str
if pathname.is_file():
tree_str += ' |' * n + '-' * 4 + pathname.name + '\n'
elif pathname.is_dir():
tree_str += ' |' * n + '-' * 4 + \
str(pathname.relative_to(pathname.parent)) + '\\... |
ed3f3de56fc8bb4bda3ddbc4c6dc923c7b46bbfcd4605f9ee454e1d868e6e922 | Python | 499 | 23 | #!/usr/bin/python3
import os
import numpy as np
from nibabel.testing import data_path
import nibabel as nib
import sys
source = sys.argv[1]
target = sys.argv[2]
aseg_filename = os.path.join(data_path, source)
A = nib.load(aseg_filename)
A_data = A.get_fdata()
print(A)
A_data[np.where(A_data == 42)] = 1
A_data[np.... |
2c45b0f1809c32411191a9138fff5e0e7f505b696328eabd2082b58d95a65aff | Python | 501 | 18 | # Copyright (c) Open-MMLab. All rights reserved.
__version__ = '0.1.1'
def parse_version_info(version_str):
version_info = []
for x in version_str.split('.'):
if x.isdigit():
version_info.append(int(x))
elif x.find('rc') != -1:
patch_version = x.split('rc')
... |
3f8dda2133f3b8f72b564f6c775cc69d998b56b49a2f37ac2986a13412f5724c | Python | 501 | 19 | import unittest
from ogo.cli.Procrustes import Procrustes
class Test_Procrustes(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tests,... |
627ceeeabd35121af4e3b3e01a475095b1166826313786e43bc57a2e71b62092 | Python | 501 | 19 | import unittest
from ogo.cli.AnalyzeBMD import AnalyzeBMD
class Test_AnalyzeBMD(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tests,... |
e136293cb1979bed752085887c98368500566bfb45036a88b09998b913e70301 | Python | 501 | 18 | from __future__ import absolute_import
from .tfidf import TFIDF
from .textrank import TextRank
try:
from .analyzer import ChineseAnalyzer
except ImportError:
pass
default_tfidf = TFIDF()
default_textrank = TextRank()
extract_tags = tfidf = default_tfidf.extract_tags
set_idf_path = default_tfidf.set_idf_path
t... |
1f7cdf70d228c671d6414b8068b07c98f5ea158dc3e90d2829533c4001357b65 | Python | 502 | 21 | """
eTSC Models Package
All model definitions
"""
from .resnet3d import ResNet3D18, ResNet3D34
from .resnet3d_dual import DualResNet3D
from .efficientnet3d import EfficientNet3DB0
from .efficientnet3d_pretrained import make_efficientnet3d_b0
from .eTSCnet import eTSCNet, LighteTSCNet
from .eTSCnet_dual import sTSCnetDu... |
57c185ca26567421491acbe54b0aecadb716cda0c54dbe0cd70c387aeb0f7b09 | Python | 502 | 24 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from typing import TypeAlias, TypeVar
__all__ = ("MaybeUndefined",)
_T = TypeVar("_T")
class _Undefined:
pass
MaybeUndefined: TypeAlias = _T | _Undefined
"""
Can be used to annotate dynamic class members that may be undefined in the object.... |
eb21a0ec911d322951cea498fdd2d470254dc4478ead71c31f61ce2cb555ea68 | Python | 502 | 22 | """ Reconstruct a surface """
import SVMTK as svm
from pathlib import Path
if __name__ == "__main__":
print("Start ",__file__)
outdir = Path("results")
outdir.mkdir(exist_ok=True)
surf = svm.Surface()
### Reconstruction Parameters ###
angular_bound=20
radius_bound=0.01
distance_... |
f8e8095dec9de18d9a898ea81821d5473964522830a2a9c26181d8f02aa3b078 | Python | 502 | 13 | from brainscore_vision import model_registry
from brainscore_vision.model_helpers.brain_transformation import ModelCommitment
from .model import get_layers, get_model
model_registry["deepeisnn_ei_cifar10_vgg19"] = lambda: ModelCommitment(
identifier="deepeisnn_ei_cifar10_vgg19",
activations_model=get_model("... |
1b297fd32402e862cb917d130f7f620d3706ba7b9b69df3bc555b92a7108db5a | Python | 503 | 14 | import torch
from .base_miner import BaseTupleMiner
class EmbeddingsAlreadyPackagedAsTriplets(BaseTupleMiner):
# If the embeddings are grouped by triplet,
# then use this miner to force the loss function to use the already-formed triplets
def mine(self, embeddings, labels, ref_emb, ref_labels):
b... |
23c42f01f28f6bf49e139d08c6f386dcd96dd29e5b74dac3a031cc4ac82b8c68 | Python | 503 | 17 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from django.urls import include, path
from rest_framework import routers
from cvat.apps.consensus import views
router = routers.DefaultRouter(trailing_slash=False)
router.register("merges", views.ConsensusMergesViewSet, basename="consensus_merges")... |
2d50be8a000f4ed9e1271a2ad90f232252b2e0f272c27fe70cf0e215cd1e4bb1 | Python | 503 | 15 | # Copyright (C) 2019-2022 Intel Corporation
#
# SPDX-License-Identifier: MIT
from cvat.apps.engine.label_colors import hex2rgb
def make_colormap(instance_data):
labels = [label for _, label in instance_data.meta[instance_data.META_FIELD]["labels"]]
label_names = [label["name"] for label in labels]
if "b... |
0d0064baff4cfcf7ab3aff44d83d6495b40c3c9d661b21f2eb6cb3000c6ea63a | Python | 504 | 23 | #!/usr/bin/python3
import os
import numpy as np
from nibabel.testing import data_path
import nibabel as nib
import sys
source = sys.argv[1]
target = sys.argv[2]
aseg_filename = os.path.join(data_path, source)
A = nib.load(aseg_filename)
A_data = A.get_fdata()
print(A)
A_data[np.where(A_data == 43)] = 1
A_data[np... |
1ed4c376420c8017d89c78d7eb7f33bd0c1abf1bfa7f8158b0536e6b0007a48a | Python | 504 | 15 | import pandas as pd
from pathlib import Path
version_id_path = Path(__file__).parent / 'version_ids.csv'
version_id_df = pd.read_csv(version_id_path, index_col='Unnamed: 0')
def build_filename(identifier: str, file_type: str):
if file_type == '.nc':
filename = f'assy_{identifier.replace(".", "_")}.nc'
... |
b64cdbf8893b9fedbc67b3867872f0bd67e9dcf78011c0a3c7cf516f1a80fd26 | Python | 504 | 18 | import sys
import subprocess
from glob import glob
import os
script = 'preprocessing/lick_extraction/lickarts_from_piezo.py'
mat_dir = 'ZENODOPATH/preprocessing/licktraces'
pathpath = 'PATHS/lickdet_piezo_paths.yml'
allfiles = glob(os.path.join(mat_dir,'*.mat'))
allfiles = [os.path.join(mat_dir,'%s-probe0.mat'%tag) fo... |
35a362d9e283022323af46d26135a6f68dc41d86f9e60c2135e8c03215f208b4 | Python | 505 | 19 | import unittest
from ogo.cli.PrintLabels import PrintLabels
class Test_PrintLabels(unittest.TestCase):
def setUp(self) -> None:
""" Use this method to prep data or files for other tests, if necessary. """
pass
def tearDown(self) -> None:
""" Use this method to clean up after the tes... |
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