sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0021b3051e790de2c07a26ef1a72c7f3d8c20c0367f444f4bc315d82ab73544b | Python | 6,639 | 179 | from typing import Callable, List, Optional, Tuple
import torch
from torch import Tensor
from torch_geometric.nn.aggr import Aggregation
from torch_geometric.nn.inits import reset
from torch_geometric.utils import scatter
class ResNetPotential(torch.nn.Module):
def __init__(self, in_channels: int, out_channels:... |
9dbb600c61088c0c9e033af33ac4f00748ef3a85c8a9b0732f426ad36a92b08f | Python | 6,640 | 186 | import json
import subprocess
from pathlib import Path
from typing import Optional
import click
import nibabel
import numpy as np
import pydicom
import simple_mri as sm
from loguru import logger
VOLUME_LABELS = [
"IR-modulus",
"IR-real",
"IR-corrected-real",
"SE-modulus",
"SE-real",
"T1map-sca... |
82fd990685a10fa80e26133d437c4d7f8cc531fea13819a8c7ed4ad0f449266f | Python | 6,641 | 187 | import cupy as cp
import numpy as np
import cupyx.scipy.ndimage as ndimage
import logging
logger = logging.getLogger(__name__)
def find_center_vo(tomo, dark, flat, ind=None, smin=-50, smax=50, srad=6, step=0.25,
ratio=0.5, drop=20):
"""
Find rotation axis location using Nghia Vo's method. :... |
c5e470d39b3031c5bc466ae354e5fcf919c1a366e82c9e9b7dbf1215e3237929 | Python | 6,641 | 130 | import json
from pathlib import Path
import logging
from brainscore_vision.utils import fullname
from brainscore_core.plugin_management import import_plugin
from brainscore_vision import load_benchmark
from brainscore_vision.model_helpers.brain_transformation.temporal import TemporalAligned
from brainscore_vision.model... |
d8d8eb36541a1208936a87cdf9ce6a78b53e482149bc13c2f78b060d9ce50ae4 | Python | 6,642 | 178 | #! /usr/bin/env python3
import subprocess
import os
import sys
os.environ["SUBJECTS_DIR"] = "/media/miplab-nas2/Data/Karolis/huppi_high_res_resting/derivatives/freesurfer/"
script_dir = "/home/degutis/dynamicConnectivityMovieWatching_2025/src/preprocessing/fmri-analysis/library"
os.environ["PATH"] += os.pathsep + scri... |
ac0dd63364bcd8af470580519e16602f6ebdbdd29a1c4a5912fc010b7e64cc36 | Python | 6,643 | 205 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""This contains the psychological models that work on images
"""
import pickle
from itertools import product
import os
from progress.bar import Bar
import numpy as np
import torch
import torchvision
import cornet.cornet_s as cornet_s
import resnet.resnet as resnet
import... |
48f470dc72d3618a37d446ef569333824016f32ab74ab4b5c202e42a73235fef | Python | 6,645 | 219 | import pandas as pd
import numpy as np
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from torchvision.transforms import Compose
import pytorch_lightning as pl
from pytorch_lightning.loggers.neptune import NeptuneLogger
from pytorch_lightning.callbacks import ModelCheckpoint
from sklearn... |
5da2d8221775279b3797962e9f9c1f5d18170c1b8e6cb6854d044c8a61287eac | Python | 6,645 | 194 | import torch
import numpy as np
from scipy.stats import rankdata
from einops import reduce, rearrange
from sklearn.feature_extraction.image import grid_to_graph
import rootutils
rootutils.setup_root(__file__, indicator=".project-root", pythonpath=True)
from src.rsa import get_phase_img
def batched_pearsonr(x, y):
... |
70143712d1c1d6ce9d0a9077dd5e26900169d7e07613e50607bc80f7d0101927 | Python | 6,646 | 156 | #! /usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Re-order one or many connectivity matrices' rows and columns. The connectivity
matrices can come, for instance, from scil_connectivity_computes_matrices.
To state the new order, use a text file with the following formatting:
The first row are the new x order and the ... |
7dd8a4ad8b21a10ad17cbf7058568d7845f67c2dc1c3284629321547341ee261 | Python | 6,647 | 119 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'mosaic_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.11.2
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.set... |
e1aaff4833c47a34249e6012fc2536714c96bd172a0a841a08ff0ccc8e1db9d0 | Python | 6,647 | 152 | import os
import fnmatch
import json
import math
import pandas as pd
# from pandas import DataFrame
def find_and_remove_substring(s, a, b):
start = s.find(a) + len(a)
end = s.find(b)
substring = s[start:end]
return substring
# 批量打开JSON文件
outputfiles_path = f'outputs/snnresnet18_split32c_b64_sn... |
4ba75742757406e6fa03653b23aaa8e32f13cc53c1e5d24bc97c58fc7b116184 | Python | 6,648 | 167 | # /------------------------------------------------------------------------------+
# | 09-MAR-2023 |
# | Copyright (c) Bone Imaging Laboratory |
# | All rights reserved ... |
8509048dbbfc7f4a35c6a4b3ccebb7395facb17d470782dbdb46d6b595386ae6 | Python | 6,651 | 140 | import os
import itertools
import pandas as pd
import numpy as np
def extract_benchmark_data(input_file):
'''
Extracts the essential information (parameters, specific runtimes)
from log file.
Parameters
----------
input_file : str
Name of the log file.
Returns
-------
extrac... |
fc18221c8852b03479451a4fde2c5fc18427a4ef44afa903d666e4a35086a6b3 | Python | 6,651 | 113 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'steve.ui'
#
# Created by: PyQt5 UI code generator 5.11.2
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow... |
d9a02e9df06191ca55012f6491b1c17b42a320745f5a9e12401222de69d34618 | Python | 6,652 | 169 | # We reuse a fraction of code in http://bitbucket.org/omerlevy/hyperwords.
# Using the numpy and similarity matrix largely speed up the evaluation process,
# compared with evaluation scripts in word2vec and GloVe
import numpy as np
import argparse
import random
from scipy.sparse import dok_matrix, csr_matrix
... |
dbc95f97be41f355a9f7a528bc06e5f68815cf60812230f5b4f02fda8e2c0ac3 | Python | 6,652 | 177 | # 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, ... |
6b6d717f91564f98d24c2ecc6f5c026812ae82439a10d6bbd3ae3fe8b7207ee1 | Python | 6,655 | 183 | import subprocess
import os
from pathlib import Path
import shutil
import numpy as np
import ase
from ase.io import read as ase_read
from chemgraph.models.graspa_input import GRASPAInputSchema
from langchain_core.tools import tool
_file_dir = Path(__file__).parent / "files" / "template"
@tool
def run_graspa(graspa_i... |
466c9d9a5ab2f0860c075447d893278f61059b432dae99cdee08ee0e5bce8207 | Python | 6,656 | 176 | # -*- coding: utf-8 -*-
"""Decoding tools for functional magnetic resonance imaging data. Execute via the
command line with python -m fmri_decoder <args>."""
import argparse
import os
from pathlib import Path
import numpy as np
import fmri_decoder
from fmri_decoder.data import DataConfig, ModelConfig, SurfaceData, T... |
dfc50ee7229df541b128b1ab3c56d87c2a57bc7a250499ab9efb6c5894b717c9 | Python | 6,656 | 185 | from typing import TYPE_CHECKING, Literal, NewType, cast
import torch
from torch import nn
from eir.models.fusion import (
fusion_attention,
fusion_default,
fusion_identity,
fusion_mgmoe,
)
from eir.models.fusion.fusion_default import al_features, default_fuse_features
from eir.models.fusion.fusion_id... |
d99549c1f32131ce388cf05bbaae33a520f4b4e5f60f4cc06e8fb78cacd15bb7 | Python | 6,657 | 140 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import tempfile
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(),
keys=['filtering.zip', 'tractogram... |
4637726cfb9371e605aa93ea372cf68dca0b3e06aa152a366f8ca1a8054f192c | Python | 6,659 | 166 | """Stop scrolling *past* a settings field from changing what it says.
A spin box or a combo box takes the wheel whenever the pointer happens to be
over it. On a tab that is itself a scrolling column of settings — which is most
of them — rolling the wheel to get further down the page silently retunes
whichever field th... |
9449a531b89ebd8288a136129252c69268d25c00b0ee084c5b3e4750af8d790a | Python | 6,659 | 205 | from __future__ import annotations
import importlib
import json
import os
import shutil
import threading
from collections.abc import Callable
from collections.abc import Iterator
from http.server import BaseHTTPRequestHandler
from http.server import ThreadingHTTPServer
from pathlib import Path
import imgviz
import py... |
516de958850d02b5e229b16ddb83a02b2fac3c6966d19fade6136c736b2b2a18 | Python | 6,661 | 195 | import os
import shlex
from app.project_e.image_processing.utilities.utils import eleSubprocess
from flask_socketio import SocketIO
def ants_registrator(
fixed_image, moving_image, outputmat, transformationalgorithm="rigid"
):
# ants call parameters
dimensionality = "-d 3"
initial_moving_transform = ... |
53e9c3fc3577ffdd1a1dab2b79a99270e9ff63a03ee66542983731c533c7b705 | Python | 6,666 | 212 | #!/usr/bin/env python
#
## @file
#
# GUI for control of Holoeye SLM.
#
# Hazen 07/14
#
import numpy
import sys
from PyQt5 import QtCore, QtGui
import storm_control.sc_library.parameters as parameters
import storm_control.sc_hardware.holoeye.holoeyeSLM as holoeyeSLM
import storm_control.sc_hardware.holoeye.holoeye_u... |
cc3a161e71f1716b5fa5172163563d65dc2e4443c48a75d6dd30ebbe331dc06f | Python | 6,667 | 172 | # Copyright (C) 2021-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import json
from http import HTTPStatus
from typing import Literal
import pytest
from cvat_sdk.api_client import models
from cvat_sdk.api_client.api_client import ApiClient, Endpoint
from cvat_sdk.core.hel... |
3b98e2324cdd252a5fbe4a6afc8fc77f977bc24542c6e6bfa318d54fb9dc6e0e | Python | 6,668 | 216 | """
Collect subject amounts for the splits used during evaluations.
This script analyzes data splits to collect statistics about:
- Subject amounts per label
- Camera IDs used
- Pixel amounts per label
- Pixel amounts per subject and label
"""
from typing import Any
import numpy as np
import pandas as pd
from htc im... |
6e56e8ec558a4174354d61f9e989dd2e987e537af05e2e99c1c3f020ff6d3b41 | Python | 6,669 | 166 |
""" Classes and functions for fitting ivim model """
import numpy as np
from scipy.optimize import curve_fit
from dipy.reconst.base import ReconstModel
from dipy.reconst.multi_voxel import multi_voxel_fit
from dipy.utils.optpkg import optional_package
class IvimModelSubtracted(ReconstModel):
def __in... |
7c58ee723d3f1f81a292d240e80fcf0160a8dbe76f9e194c95ee1c787ed51cb7 | Python | 6,669 | 234 | import numpy as np
import polars as pl
from eir.data_load.storage_engine import NULL_STRINGS, HybridStorage, is_null_value
def test_nan_preservation_in_numeric_data():
df = pl.DataFrame(
{
"ID": ["sample1", "sample2", "sample3"],
"float_col": [1.5, np.nan, 3.5],
"int_c... |
f5064fd7ee1625951536990f32aa2c89720ca670a9dc0b5b45922ae5626ce1a9 | Python | 6,669 | 184 | from PUMI.engine import NestedNode as Node, QcPipeline
from PUMI.engine import FuncPipeline
# To extract voxels 10 to 12 inclusive you would specify 10 and 3 (not 10 and 12).
@FuncPipeline(inputspec_fields=['in_file'],
outputspec_fields=['out_file'])
def pick_volume(wf, volume='middle', sink=True, **kw... |
18de04c22d20b3aa621d505fc8e522345acbf7baa2cd79a908cd77ab8fe1ec8e | Python | 6,670 | 146 | # -*- coding: utf-8 -*-
"""
Created on Fri Jun 25 16:58:13 2021
@author: Yoshi
"""
import os
import shutil
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as stats
import math
from PIL import ImageColor
def correlation_matrix(path,data,cell_flags,framerate_information,extra_flag,mode=0):
... |
d3a12c2cbe336865cf4678f10057a16ab76c99dbaf9c3c9d044c5893da957bf9 | Python | 6,670 | 164 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Projects maps extracted from a map onto the points of streamlines.
The default options will take data from a nifti image (3D or 4D) and project it
onto the points of streamlines. If the image is 4D, the data is stored as a
list of 1D arrays per streamline. If the imag... |
4c02ee31ecd1990367e97f0017bcc54ac170bbd0e34332eef2f3aaf7dcbffd57 | Python | 6,672 | 198 | #Lucas Sancéré -
"""
Here we will add the functions from classic_image_processing
from Misc_Utils othat are needed (probably downsampling code and so on) and are not present anywhere on this repo
"""
import glob
import os
import PIL
from PIL import Image
from tqdm import tqdm
PIL.Image.MAX_IMAGE_PIXELS = 1000000000... |
86ded150909a2a131df51fd6c624187884e96e786146daad27c5224f1c6ce0d4 | Python | 6,672 | 186 | """Deep Agent action-review cards for the Streamlit chat.
The CLI renders each pending tool action (shell command, file write, file
edit, ...) as a panel and asks for approve/reject. This module gives the
chat the same information as cards with buttons. ``action_preview`` is
pure and mirrors ``chemgraph.cli.formatti... |
fcb7677fbb5794a2e931fc8d249af3df356bae7ac5dc4e39424ca0ed37f2db78 | Python | 6,672 | 184 | # -*- coding: utf-8 -*-
# @Author : LG
import os
from json import dump, load
from typing import List, Union
import numpy as np
from PIL import Image
from ISAT.utils.dicom import load_dcm_as_image
__all__ = ["Object", "Annotation"]
class Object:
r"""A class to represent an annotation object.
Arguments:
... |
839f0c8b1dfb8d36f2a214d8beaeb9630b41c7fafa86539356d707c92c49abf3 | Python | 6,674 | 120 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '/media/lg/disk2/PycharmProjects/ISAT_with_segment_anything/ISAT/ui/category_setting_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.15.10
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not... |
66df4523466d2a40b3e0ebd5367efee1f7fedea2eddcce05e659a2922bfcb762 | Python | 6,676 | 138 | import numpy as np
from result_caching import store
from brainscore_core.supported_data_standards.brainio.assemblies import DataAssembly
from brainscore_vision import load_dataset, load_metric
from brainscore_vision.benchmark_helpers.properties_common import PropertiesBenchmark, _assert_texture_activations
from brains... |
937ccd3e6ac4d1f5e4e82d0d0233335c9185737e483cd08a547ddeb5ac926717 | Python | 6,676 | 189 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Maximilian Betz, Daniel Richter
#
# 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 compli... |
3f10ac62582fd471b2792d1abcebc44c68cd75ccfc1975d5fe8791ac67188ab7 | Python | 6,677 | 151 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or... |
a6f5213b05d0e9e955d972afb599601be00f31cccec0eea4bafe671c8546c01b | Python | 6,677 | 154 | #!/usr/bin/env python
# coding: utf-8
'''
Dependencies:
pip install pandas numpy voxcell matplotlib scipy
External dependencies: calculate_density_mm3(), get_all_filenames(), get_csv_filenames(), extract_prefix_from_filenames()
chmod +x script.py
In this code we're going to improve region coverage which is already b... |
22148d9d175ba7228e6755b03d1e68ba403ad5009f1865954ee034b11adea01b | Python | 6,680 | 197 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import json
from collections.abc import Callable, Mapping
from typing import Any, TypeAlias
__all__ = ["Condition", "F", "Field", "Filter", "JsonLogicExpression", "all_", "any_", "not_"]
JsonLogicExpression: Type... |
511233a039e2e311c0b7feae2f6e92c350328520b9f4267bab0015e8d51be5f5 | Python | 6,682 | 179 | # adapted from mtbatchgen by Zahoor
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import os
from collections import OrderedDict
import deepdish
import modisco.visualization
from modisco.visualization import viz_sequence
import h5py
import numpy as np
import modisco
#import modisco.backend
#im... |
b448886b41128a06b99ab8b2ab321aa93c00ecbf3c17321de1114589a70d2e85 | Python | 6,682 | 150 | # ==============================================================================
# Binaries and/or source for the following packages or projects are presented under one or more of the following open
# source licenses:
# MinCostFlow.py The OpenLane Dataset Authors Apache License, Version 2.0
#
# Contact sim... |
b344d0903cd54d3e1f2aff572372abae6a34dce44a07ffefe285d4315144e994 | Python | 6,683 | 158 | # Copyright (c) 2022, Kwanhyung Lee. All rights reserved.
#
# Licensed under the MIT License;
# you may not use this file except in compliance with the License.
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTI... |
64d955ea491c58893c3bab671f33b9d8f9fa750f3f84bbebc952acea70b416e8 | Python | 6,685 | 178 | # 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.
import torch
from torch import nn
from torch.nn import functional as F
from typing import List, Tuple, Type
from .common... |
613864e7e917536e39e7a36ea6439139ad71c9fde8476dd27854ed5e722df02c | Python | 6,686 | 201 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import math
from typing import Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
try:
from timm.layers import DropPath
except ModuleNotFoundError:
# compatibility for older timm versions
from timm.models.layer... |
7b7c69a2b8857f2533cd0462f55490efc78c960cb45417b534c6f4d043ebaa9d | Python | 6,686 | 202 | #!/usr/bin/env python
# Copyright 2017 Calico 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 ... |
d182c8e83bff7b175e83f755f39560073b15923766e19eee803725ccb68052c4 | Python | 6,687 | 221 |
import torch, torch.nn as nn, torch.utils.data as data, torchvision as tv, torch.nn.functional as F
import pytorch_lightning as L
import numpy as np
from torch.utils.data import Dataset, DataLoader
from sklearn.metrics import roc_auc_score
from pytorch_lightning.callbacks import ModelCheckpoint
class modulerNetwork2... |
1a47e6a3a116f9f9d9d24bd4a8303312fc62aaa14c7d3bc221036018b0d9696b | Python | 6,691 | 216 | import torch
import torch.nn.functional as F
from torch.utils.data import Dataset
import polars as pl
import numpy as np
from random import randrange, random
from pathlib import Path
from pyfaidx import Fasta
# helper functions
def exists(val):
return val is not None
def identity(t):
return t
def cast_list... |
4d588e13d32e2b7bf2ecc18348c385c99b410c07ac764eb1e856c0ff10de1020 | Python | 6,691 | 214 | from itertools import chain
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from eir import train
from eir.train_utils.utils import seed_everything
from tests.conftest import should_skip_in_gha_macos
from tests.setup_tests.setup_modelling_test_data.setup_sequence_test_data import (
get_con... |
6861430d377f68b70d3f9ed9f951a0b3d84988804cbddbde2e50b1da5ac08ed9 | Python | 6,691 | 229 | #!/usr/bin/env python
# A script to run simulations sequentially.
# Copyright F. Nedelec, 2010--2018
# Using multiprocessing thanks to Adolfo Alsina and Serge Dmitrieff, March 2016
"""
Synopsis:
Run simulations sequentially.
For each config file, a simulation is started in a separate 'run' directory.
... |
8d910888fc8974f1f57c181cac4849780120c9012fa9763086cd54dd5d265fc8 | Python | 6,691 | 213 | import pandas as pd
import numpy as np
import argparse
import os
import argparse
import os
import os.path as osp
import matplotlib.pyplot as plt
print("calculating the branching angles!!")
# cf.: https://arxiv.org/pdf/1803.09340.pdf
# cos(phi_l) = rp^⁴
# cf. https://stackoverflow.com/questions/62888678/saving-a-3d-... |
cef1b19646ad5397a9610fc2bfc20598b3a9316732acbb096904a6e4c105f1cb | Python | 6,691 | 155 | import os
import os.path as op
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib.gridspec import GridSpec
import seaborn as sns
sys.path.append('/imaging/hauk/rl05/fake_diamond/scripts/preprocessing')
sys.path.append('/imaging/hauk/rl... |
fce415c6bd9e932bad5550b803e27aabec1473a5365a8247415137c0f56263d1 | Python | 6,696 | 150 | """Stimulation-analysis step of the pipeline (MEA-Stim).
Runs right after spike detection (step 1) when ``params.stimulation_mode`` is
set, mirroring MATLAB's ``MEApipeline.m`` — where ``batchDetectStim`` +
``batchProcessSpikesFromStim`` run at the end of step 1 and
``stimActivityAnalysis`` + ``saveEphysStatsStim`` at... |
1210995f725cf80a3a5c317a4a1b3c4337ac1d31c7fca6a65764fb1c66962d26 | Python | 6,697 | 191 | # Copyright (c) DP Technology.
# 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.
import torch
from unicore import utils
class UnicoreOptimizer(object):
def __init__(self, args):
s... |
843e2600630e0ad655e2a7a5adc681c70d2d4a91d546056bf0e3331f512b64a5 | Python | 6,697 | 187 | from typing import List, Union, Dict, Tuple
import numpy as np
from napari.utils.notifications import show_info
from bg_atlasapi import BrainGlobeAtlas
def get_bregma(atlas_id: str) -> List[int]:
"""
Definition of bregma coordinates for different atlases.
Parameters:
atlas_id (str): The atlas ID... |
8d4fc6343d37e7978024cbe84ce449dbb7313c7b55730a615117f03f0eeda0fa | Python | 6,698 | 184 | from __future__ import division
from enum import IntEnum
class ElementTags(IntEnum):
TH_START = 0
WM = 1
GM = 2
CSF = 3
BONE = 4
SCALP = 5
EYE_BALLS = 6
COMPACT_BONE = 7
SPONGY_BONE = 8
BLOOD = 9
MUSCLE = 10
ELECTRODE_RUBBER_START = 100
ELECTRODE_RUBBER = 100
EL... |
aa32f2f2836bf4aac9bcf02482cd36c68b5805785dfdbda284797ae3cf98d1e6 | Python | 6,699 | 290 | import torch
import numpy as np
import pandas as pd
from datetime import datetime as dt
from dataset import fast_merge,df_to_mask
from tqdm import tqdm
dataset_names = [
'botometer-feedback-2019', 'botwiki-2019', 'celebrity-2019', 'cresci-2015', 'cresci-2017', 'cresci-rtbust-2019', 'cresci-stock-2018', 'gilani-2017... |
d4510794a730565c293d0b8e734854c25aad9b00cb787a9f0f45e02bb0c65fe2 | Python | 6,700 | 205 | import torch
from typing import Optional
def initialize_tensor_like(
src: torch.Tensor, shape: int, fill_value: float = 0.0
) -> torch.Tensor:
"""
Initialize a tensor with provided shape and same dtype and device as src.
By default initializes with zeros.
"""
out = torch.full(
shape,
... |
2a4ec9052f13225556b0513ca3d88580def427320e24d989a97ad65af0b1a5bd | Python | 6,701 | 146 | from typing import Optional
import torch
from torch import nn
from torch import nn, Tensor
from torch.nn.modules.transformer import _get_activation_fn
def add_ml_decoder_head(model):
if hasattr(model, 'global_pool') and hasattr(model, 'fc'): # most CNN models, like Resnet50
model.global_pool = nn.Identi... |
a92db89f95c9af67e9b6753b5b80f460b39d7f3c9626cc4a45d2725a5a801133 | Python | 6,705 | 255 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import warnings
import re
import fnmatch
import psutil
import pandas as pd
import numpy as np
import ants
from aicsimageio import AICSImage
from glob import glob
from tqdm import tqdm
from readlif.reader import LifFile
import mbflim.shared as sha
def has_han... |
d9f701357ad1dbc056addf9a44a4d29114380417c73b87cbbd0b24f521113a19 | Python | 6,705 | 151 | import numpy as np
import xarray as xr
from brainscore_core.supported_data_standards.brainio.assemblies import NeuroidAssembly, array_is_element, walk_coords
from brainscore_vision.metric_helpers import Defaults
from brainscore_vision.metrics import Score
class XarrayRegression:
"""
Adds alignment-checking, ... |
1f094217c00eca801afc3de0a02b12c63d53ec731263dcaf6b6d6bff024b6a1e | Python | 6,706 | 155 | # -*- coding: utf-8 -*-
# python standard library inputs
import os
import shutil as sh
# external inputs
from nipype.interfaces.fsl import FLIRT
from nipype.interfaces.fsl.preprocess import ApplyXFM
from nipype.interfaces.freesurfer.preprocess import MRIConvert
from nighres.registration import apply_coordinate_mappin... |
5fa76758040f4eacadce46aefef48436ecd05488506bd52a71883a04c3384f5f | Python | 6,707 | 183 | import warnings
import numpy as np
def minmax(x, floor=1e-6, warn_on_nan=True, inplace=False):
"""Normalize array `x` within each output channel to have min 0 and max 1.
For array `x` with `x.ndim == m` and `x.shape == (d_1, d_2, ..., d_m)`, the
first `m-1` dimensions of `x` will be flattened. Minim... |
6d913321af27e6da06645d03d1bce9bbacbaaa67d4c18443bd98d14e4a64ca87 | Python | 6,707 | 199 | #!/usr/bin/python3
#
import os
import sys
import argparse
import shutil
from copy import deepcopy
import numpy as np
from sklearn.neighbors import NearestNeighbors
from uac import utils
# Create the parser
my_parser = argparse.ArgumentParser(description="UAC fibre mapping")
# Add the arguments
my_parser.add_argument... |
2958d5d9bba749f14700f4927091a79578d2ef83415f4bdc9d32c8f7c4892032 | Python | 6,708 | 197 | import numpy as np
from pandas import DataFrame
from collections import defaultdict
from scipy.spatial.distance import cdist
from . import plot_utils
from . import data_utils
import matplotlib.pyplot as plt
def insulation_mask(h=1):
mask = np.zeros((32,128))
h = int(32*h)
for i in range(h):
... |
1a3f7eb499e9c903ccca2c6383bb0d70a6637b52f7045324f88f582173a72d01 | Python | 6,709 | 224 | from collections.abc import MutableMapping
import numpy as np
import scipy.io as sio
from ..structures import PLSResults
_result_mapping = (
("u", "x_weights"),
("s", "singvals"),
("v", "y_weights"),
("usc", "x_scores"),
("vsc", "y_scores"),
("lvcorrs", "y_loadings"),
# permres
("perm... |
4a47f07ea0ffd41e3e61a9f632f30d1a3f7e046fe7335e795a8311a43ed61005 | Python | 6,709 | 153 |
def calculate_movement_directions(kymo, movement_threshold, time_threshold):
left={};
right={};
stat={};
reversals={};
# Initialising result dictionary
for track in kymo.keys():
left[track] = [];
right[track] = [];
stat[track] = [];
reversals[track] = [];
... |
3653ea29144c822d7eb4b6633d155082c88b35c384a58ba7654939e22adb4e49 | Python | 6,712 | 220 | import functools
import json
from abc import ABC, abstractmethod
from contextlib import ExitStack
from http import HTTPStatus
from time import sleep
from typing import Any, TypeVar
import pytest
T = TypeVar("T")
from shared.utils.config import get_method, post_method
FILENAME_TEMPLATE = "cvat/{}/{}.zip"
EXPORT_FORM... |
8b897ddb523a49430f12844e83b12e25f82a2b8ee8be618eee8f8661aadc9a80 | Python | 6,712 | 175 | # -*- coding: utf-8 -*-
"""
Created on Fri Oct 20 09:06:04 2023
@author: lcmmichielsen
"""
import numpy as np
from tqdm.notebook import tqdm
import seaborn as sns
from matplotlib import pyplot as plt
def plot_peaks_RBP(RBP, exons_info, peaks, PSI_glia, PSI_neur,
lowthres=0.5, highthres=0.5, save=... |
45e2c726371c8108331ee7484c7d5960f74cf7daf8128feb68c400afb55d734d | Python | 6,713 | 169 | # Kai Sandbrink
# 2022-10-18
# Script that loads configuration options and runs training loop
# %% LIBRARY IMPORTS
import torch
import numpy as np
import torch.multiprocessing as mp
import copy, time
from utils import Config
from trainers import train
# %% PARAMETERS
n_runs = 5
# %% CONFIG OPTIONS
config = Conf... |
a7a2e02cb8a876e4be9d98322eeea5dfd4e15cf53a5cd3fc59b620d6c541bfd1 | Python | 6,713 | 145 | 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
from nipype.utils.filemanip import split_filename
from nipype.interfaces.base import ... |
d5c449c30bfde92457b9c1feb9d871c61bce43bc85bc6d13e478630b05018024 | Python | 6,713 | 158 | import numpy as np
import torch
from torch import nn
class CNNRNN(nn.Module):
"""
Maybe further ideas:
https://www.kaggle.com/c/rsna-intracranial-hemorrhage-detection/discussion/117210
https://www.kaggle.com/c/rsna-str-pulmonary-embolism-detection/discussion/194145
For this to train properly need... |
5a4fbbdcd38852e35cfec4ec71ea2ae0243960b9cfd1b98f95992382558d5709 | Python | 6,714 | 162 | # Copyright (C) 2021-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import functools
from allauth.account import app_settings as allauth_settings
from allauth.account.internal.flows.email_verification import send_verification_email_for_user
from allauth.account.models impo... |
0f2e2e1199533194b4fa5374a4186a12d573ac7767a31581121edab5e85e6efa | Python | 6,715 | 148 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
"""Synapse removal module."""
import numpy as np
from scipy.sparse import csc_matrix
from connectome_manipulator import log, profiler
from connectome_manipulator.access_functions impor... |
ed989b7f9d52289b398fa3fb8b23e7a09c4d92e3612566c1e669d2ff57092a8e | Python | 6,715 | 181 | from argparse import ArgumentParser
from dataset import SATARDataset
import numpy as np
import time
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from model import SATAR, FollowersClassifier
from tqdm import tqdm
from utils import null_metrics, calc_metrics, is_better
device = torch.device... |
f904ecc72c3f1cfcf93828c6ea626de1aa9c891f290a20a304264711ea0f967e | Python | 6,715 | 218 | # -*- coding: utf-8 -*-
"""
Interface to write points to VTK files
Notes:
- points are assumed to be in [x,y,z] coordinates as standard in ClearMap
- reading of points not supported at the moment!
"""
#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New York City
#:license: GNU, see... |
8043124d1d494817175e7d3b1664d34f80dbb3a3328f7908bdf94516f39db9d9 | Python | 6,716 | 196 | from collections.abc import Callable
from dataclasses import dataclass
from functools import partial, update_wrapper
from pathlib import Path
from typing import Any
import numpy as np
import polars as pl
import torch
from PIL.Image import Image
from eir.data_load.data_preparation_modules.input_preparation_wrappers im... |
97924d854794ab9bd6c232d87d473a34693c3d121865ca043d7c4973a914ecb9 | Python | 6,716 | 139 | import pandas as pd
import numpy as np
import os
## Read in data
# cd ./reproduce/synleth/
# Define threshold and directory name
THR = 0.90
DIR_NAME = "KR4SL_thr0{}".format(str(THR).replace('.', '').lstrip('0'))
# Define input and output directories
input_dir = f"./{DIR_NAME}/data/transductive/original/"
output_dir... |
0193c83d8131030b328b85879e0b2f67fb3e3abe67a42265c185492350005f88 | Python | 6,717 | 217 | #!/usr/bin/env python
"""
These classes render the graph / image for the spot
counter.
Hazen 05/17
"""
import numpy
from PyQt5 import QtGui, QtWidgets
class SpotWidget(QtWidgets.QWidget):
"""
Spot graph / display base class.
"""
def __init__(self, shutters_info = None, **kwds):
super().__ini... |
7f5c97b196b537d3d2655a082f78978d94de38d0ebd6cbead5dd1fb8590b60f3 | Python | 6,720 | 148 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
9ea265fcd1e3277209a1c7604d571e3ac6f6d87f63e63bedc3d4195ccf023d4d | Python | 6,723 | 206 | from __future__ import annotations
from collections.abc import Iterator
from pathlib import Path
import pytest
from PySide6.QtCore import QTimer
from PySide6.QtWidgets import QApplication
from PySide6.QtWidgets import QMessageBox
from pytestqt.qtbot import QtBot
from labelme._app import MainWindow
from ..conftest i... |
f064e9b56c93e05dcd70f5298d1f57a6a66b80cf2e5406108712e3de40a5068c | Python | 6,723 | 192 | """Network initialization utilities."""
from typing import Any
import torch
import torch.nn as nn
from mcmlnet.utils.logging import setup_logging
logger = setup_logging(level="info", logger_name=__name__)
def matmul_precision(precision: str) -> None:
"""
Set the precision for matrix multiplication based o... |
2c45dfaa19f5e6b27f9ffca22c5492a1c5135876381f2fe9ebf22dbc09816bb2 | Python | 6,727 | 149 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from typing import Any
import numpy as np
from ultralytics.solutions.solutions import BaseSolution, SolutionAnnotator, SolutionResults
from ultralytics.utils.plotting import colors
class RegionCounter(BaseSoluti... |
c9349e38a349e46550fefcfc13b6581a0c944b8a7f8d0a5fbcd6e58804d537da | Python | 6,727 | 147 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
be9e7bc3e597a589ef7baacc5d39e9bac848a5102465b6c0ee013df2b31048e3 | Python | 6,728 | 172 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Generation of priors and enhanced-FOD from an example/template bundle.
The bundle must have been cleaned thorougly before use. The E-FOD can then
be used for bundle-specific tractography, but not for FOD metrics.
-------------------------------------------------------... |
bf049086a305a7bd1387afce3f832f2cd4b4336ca5fb1b43ae20ada216fe653b | Python | 6,728 | 231 | """ Various functions related to calculations with arbirary gradient waveforms. """
import numpy as np
import numpy.typing as npt
from ivim.constants import y
def q_from_g(g: npt.NDArray[np.float64], dt: float) -> npt.NDArray[np.float64]:
"""
Calculate the dephasing vector for gradient waveform g.
Argume... |
323f8df06b51983c1032a0a1ca3a5b2ab9b8c34cccdc82c8925ec9288c4bc590 | Python | 6,729 | 169 | #New:
from __future__ import print_function, absolute_import
import os.path as osp
import glob
import re
from ..utils.data import BaseImageDataset
class Market1501(BaseImageDataset):
"""
Market1501
Reference:
Zheng et al. Scalable Person Re-identification: A Benchmark. ICCV 2015.
URL: http://www... |
81a2364d0fdedbf7351ec3055cdff11f0da0d5cf16b9afb3f0fad51e526f4ae7 | Python | 6,729 | 232 | import distinctipy
def is_valid_color(color):
"""Returns True is color is length 3 (r,g,b) with each element between
0 and 1."""
return len(color) == 3 and all([x >= 0 and x <= 1 for x in color])
def test_get_random_color():
"""Assert all r,g,b components are between 0 and 1"""
color = distincti... |
1c81d26fd67996cab2cb4fb0869b2e15268b944a217c545f2eb8eb5dffa44398 | Python | 6,730 | 172 | import os
from typing import List, Tuple, Union
import nibabel as nib
import numpy as np
from deepreg.dataset.loader.interface import FileLoader
from deepreg.dataset.util import get_sorted_file_paths_in_dir_with_suffix
from deepreg.registry import REGISTRY
DATA_FILE_SUFFIX = ["nii.gz", "nii"]
def load_nifti_file(f... |
c13298fab0f1cfb683fbd43289402645c26228d2f0e9c0a4f2da9099c2c64895 | Python | 6,730 | 147 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
d17c36ba820c896757fcf5146a2b1c8f759f7ceb6e880c9ed5c64a79d9857408 | Python | 6,730 | 179 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
"""Watch a project for newly created tasks via a webhook: register the webhook
pointing at this machine, receive the deliveries with a local HTTP server, and
tally each 'create:task' event.
The server signs every delivery with the webhook secret (HM... |
71986a4b54cdf142858b3635472b3c79edd88cd8724f1d6c98213cbdf508a0fe | Python | 6,733 | 168 | import os
import math
import tqdm
import numpy as np
import pandas as pd
import tensorflow as tf
from collections import Counter
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from tensorflow.keras.utils import Sequence
class AccelerometerDataGenerator(Sequence):
def __init__(self, subject_fi... |
dbc8b9e763ed4567afacd5329d2fae419c6aa3d2949a5e18982e36ad770e556f | Python | 6,733 | 193 | import glob
import numpy as np
import staintools
import pandas as pd
from PIL import Image
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras.models import Model
from tensorflow.keras.layers import Flatten, Dense, Dropout, GlobalAveragePooling2D
from tensorflow.keras.applications.mobilenet impor... |
2f92b5c41278338b4d68dbd44ee4376e1c28af0f98b6bd427c537c3f0d529f61 | Python | 6,734 | 219 | import os
import time
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision.transforms import v2
from torch.utils.tensorboard import SummaryWriter
""" IMPORT CONFIG """
import V1_5_train_cfg
# cfg appends working directory to sys.path, so... |
57650df356e971f2aa8526c84d3fa6ddcb32b87a5fb85b0e068930b173bacd31 | Python | 6,735 | 179 | """
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... |
6e6255e1ee4febf2e63833791afaa27fcd6ec1bcf366ace25ec9990e110c66cb | Python | 6,735 | 148 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
71549beccb199122eff1253a6ae0e39a2cdbe788bfbb4959c6750f487cce4e9c | Python | 6,736 | 152 | #!/usr/bin/env python
"""
Provides the time base for a film.
Hazen 04/17
"""
from PyQt5 import QtCore
import storm_control.sc_library.parameters as params
import storm_control.hal4000.film.filmSettings as filmSettings
import storm_control.hal4000.halLib.halFunctionality as halFunctionality
import storm_control.hal4... |
a60a9ce8ec63295593c760bffe6af9f6d34501c77af0d410eba7e0807b08b8a0 | Python | 6,736 | 167 | import argparse
import json
import jax
import jax.numpy as jnp
from model import (
FullConfig,
HyperParams,
TrainingConfig,
LoggingConfig,
initialize_p,
initialize_training_state,
make_constant_gammas,
closure_draw_cs_data_driven,
train_natural_gradient_scan_over_epochs,
linear_... |
dc0e311793c8790ce9c1221e44255a83f71054d3517748d5904ac834c2fec155 | Python | 6,736 | 148 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
86e1c91c0327204b060dbf5c104d29c5b992799b44e17c1fca922b61ef9562a9 | Python | 6,738 | 147 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from brainscore_vision.model_helpers.activations.pytorch import load_preprocess_images
import torch
import torch.nn as nn
import torch.nn.functional a... |
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