sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a83072793490e7aa55ad73934c4d5c643b058cb4e74abc9dca05d7d5cc5df401 | Python | 11,609 | 180 | from brainvoice.configuration.configuration import Configuration
from brainvoice.configuration.utils import extract_modify_dict
from brainvoice.configuration.configuration_linker import ConfigurationLinker
from brainvoice.configuration.static_configuration_parser import StaticConfigurationParser
import argparse
... |
e6d235db391065fcf6ec5f847b3407e367616c938a09df3b0434355aa0082e2c | Python | 11,609 | 347 | import os
import pandas as pd
import numpy as np
import math
from numpy.linalg import norm
import MDAnalysis as mda
from scipy.stats import pearsonr
def angle(x1, y1, x2, y2, x3, y3):
# Calculate vectors BA and BC
BA_x = x1 - x2
BA_y = y1 - y2
BC_x = x3 - x2
BC_y = y3 - y2
# Calculate do... |
4e0c7f46067422919dae835defae664479fcd2e736ee4eaa7d2fdb810192ea1a | Python | 11,619 | 266 | import argparse
import logging
import sys
import os
import sys
from pathlib import Path
import h5py
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import optim
from torch.utils.data import DataLoader, random_split
from tqdm import tqdm
import torch.utils.data as Data
from utils.data_loadi... |
51030aabecc2e7da1db5d414f0d9df291dca6207ce925e064f27c6bd0eef821b | Python | 11,622 | 324 | # Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
a9e12b9ab557a7b0d7fc0304b8f13c747dd4e47263e682b38fe5f222980c9315 | Python | 11,623 | 271 | # 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 numpy as np
import torch
from .modeling import Sam
from typing import Optional, Tuple
from .utils.transforms imp... |
9822010a983c4a5bc712e853423a1241ad68958bb29d4d817a8acaa61391ee2c | Python | 11,625 | 278 | """The viewer's controls describe the run, not the viewer.
Opening a bundle used to show a generic control set: every default read off a
fresh ``NetworkStyle``. That was wrong as *display* — the panel claimed a
node-size scale of 1.0 for a CAT-NAP run drawn on ``"auto"`` — and worse as
*behaviour*, because the page se... |
cb89b2bf5a2922b58a71c073b45d3d6ef0005da6d457fe60d256e9e873668bf4 | Python | 11,625 | 429 | # -*- coding: utf-8 -*-
import ast
from colorama import Fore, Style
from importlib.resources import files
import itertools
import logging
import multiprocessing
import pathlib
import re
import subprocess
from tqdm import tqdm
import nltk
from nltk.stem import PorterStemmer
from scilpy import SCILPY_HOME
SPACING_LEN ... |
aee5863ff2c6008cda5e09c361b818ee8e08dd0ab315a096500a638a22b6b4e4 | Python | 11,629 | 338 | from __future__ import annotations
import collections
from typing import NamedTuple, Literal
import numpy as np
from matplotlib.axes import Axes
from scipy.interpolate import interp1d
from typing_extensions import Self
from argclz import argument, float_tuple_type
from neuralib.persistence import *
from neuralib.plo... |
8a051e2fd6bba95f513d513d4436cb5eb5e14aedb50e72896e68bad9945080b5 | Python | 11,630 | 355 | import os
import logging
import hail as hl
import heig.input.dataset as ds
from heig.wgs.relatedness import LOCOpreds
from heig.wgs.utils import read_genotype_data, init_hail, get_temp_path, clean
"""
TODO:
1. consider providing more preprocessing options? such as --chr
"""
def parse_ldr_col(ldr_col):
"""
... |
017d6914659fbd131da9e480415cd6b24c431b91bf15897523ffdd5f2593b19a | Python | 11,631 | 322 | from typing import NamedTuple, Literal, ClassVar, cast
import attrs
import numpy as np
import scipy
from typing_extensions import Self
from neuralib.locomotion import CircularPosition
from neuralib.typing import PathLike
from neuralib.util.interp import interp_timestamp
from neuralib.util.verbose import fprint
from r... |
f0c03df10a18b7799b32b1c12b6c671c3f367f7777fed3d56a3804726199a57e | Python | 11,631 | 373 | import numpy as np
from sklearn.metrics import r2_score
from .. import compute, utils
from ..base import BasePLS, gen_splits
from ..structures import _pls_input_docs
class BehavioralPLS(BasePLS):
def __init__(
self,
X,
Y,
*,
groups=None,
n_cond=1,
n_perm=50... |
1e6d04bd1310a3815a0c9ab0013c1881521034a797b7eae5a485215a61d7f542 | Python | 11,635 | 340 | """Functions to calculate static properties of time series data."""
import logging
from typing import Callable, List, Optional, Union
import numpy as np
from sklearn.covariance import LedoitWolf
from pqdm.threads import pqdm
from threadpoolctl import threadpool_limits
from tqdm.auto import trange
from osl_dynamics.a... |
b55699485b990636d2d60f2bdb0623f45e02a9f47f81450fcb7ba2a4c8f5c0f4 | Python | 11,636 | 303 | """Scrolling past a settings field must not retune it.
Run from the repo root::
uv run python python/test_gui_wheel_guard.py
A spin box or combo box takes the wheel whenever the pointer is over it, so
rolling down a tab of settings used to change whichever fields the pointer
crossed. The page scrolled either way... |
ca663c3078e176e80c8e88779addf127563a5805d55c6ba77e892616dbba5170 | Python | 11,637 | 374 | import itertools
import random
import logging
from collections import defaultdict
from enum import Enum
from pathlib import Path
from typing import List
from flair.data import Dictionary, Sentence
from functools import reduce
from sklearn.metrics import mean_squared_error, mean_absolute_error
from scipy.stats import pe... |
c6828856aa6399718e02c0a70efe98baab266df2849f3ddc674e32bb8cfbef03 | Python | 11,639 | 253 | import json
import os
from mako.template import Template
from sympy.parsing.sympy_parser import parse_expr
from sympy.parsing.latex import parse_latex
from sympy.printing import cxxcode
def remove_parentheses(expr):
if '(' in expr and ')' in expr:
return expr[:expr.index('(')]
else:
return exp... |
df78acd7bf722b93f56072700ced2707e7db29ce6aedb60357f716e7da9ac72d | Python | 11,645 | 341 | # Crosscheck folder names and geometry.in data
import os
import glob
import collections
import numpy.typing as npt
from modules.tools.strings import get_clus_and_mol, get_atoms_and_amount
from modules.tools.error import display_traceback
from modules.tools.xyz_tools import convert_geometry_in_to_xyz, generate_xyz
#... |
97fa56079a5f51e1e2202ef6ca1ea7b68f80eb2bc6c5116a62ff56cdc037112b | Python | 11,647 | 321 | import numpy as np
from matplotlib import pyplot as plt
from dipy.core.ndindex import ndindex
from dipy.core.geometry import cart2sphere
from dipy.core.gradients import gradient_table
from dipy.reconst.dki import _positive_evals
from dipy.reconst.vec_val_sum import vec_val_vect
from dipy.reconst.dti import (design_ma... |
f1cf57a89de9c56e5367f45a1001d999b3ba234be3b1bf51921a5710591dc3dd | Python | 11,647 | 287 | from . import PYQT5, PYQT6, PYSIDE2, PYSIDE6
if PYQT6:
from PyQt6.uic import *
elif PYQT5:
from PyQt5.uic import *
else:
__all__ = ["loadUi", "loadUiType"]
# In PySide, loadUi does not exist, so we define it using QUiLoader, and
# then make sure we expose that function. This is adapted from qt-h... |
6e79202d565106e9a625d3700dcdb036b5a8d4dc65e32bac945ff2fa5bb558cb | Python | 11,653 | 296 | import json
import numpy as np
import pandas as pd
import pytest
from metaprivBIDS.corelogic import (
add_gaussian_noise,
add_laplacian_noise,
bin_numeric_values,
calculate_k_combined,
calculate_k_global,
calculate_l_diversity,
calculate_mad_outliers,
calculate_privacy_metrics,
com... |
70a0bd4687f0d897485584a4314c6c254dd1d721228002d2c458131d66e5aedd | Python | 11,655 | 295 | """ADMET-AI class to contain ADMET model and prediction function."""
from pathlib import Path
import numpy as np
import pandas as pd
import torch
from chemprop.data import (
MoleculeDatapoint,
MoleculeDataset,
)
from chemprop.models import load_model
from chemprop.data.dataloader import build_dataloader
from ... |
6b4efdcefbd18fbd9b1ffa709aa8a2133bab385b52108d298708a628747ca591 | Python | 11,661 | 287 | # train.py
import argparse
import os
import torch
import torch.optim as optim
import numpy as np
import torch.distributed as dist
from torch.nn.parallel import DistributedDataParallel as DDP
from monai.losses import DiceCELoss
from monai.inferers import sliding_window_inference
from monai.data import DataLoader
from tq... |
404ba8112000e3085c17f4251f4171efa487461be7902e1963acbdc0d0b21d4f | Python | 11,663 | 302 | # -*- coding: utf-8 -*-
# fashion_mnist_td_vs_baseline.py
import copy, random, os
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader, random_split
from torchvision import datasets, transforms
import matplotlib.pyplot as plt
# =====... |
6129a69fa1e79a3bde75c562fbe42a9c29138e2eeca657c7b3c82da7a6a3fe6f | Python | 11,664 | 333 | #! /usr/bin/env python3
"""
Implements function find_roi and corresponding nipype interface FindRoi and command line interface.
"""
import sys
import os
from scipy.optimize import bisect, brentq
from nipype.interfaces.workbench import MetricResample
from nipype.interfaces.base import (
BaseInterfaceInputSpec,
... |
d5bbd05dbcf111a94bf35601e7352ba1f38660db731b91dc2cdf1062873718c0 | Python | 11,664 | 295 | import numpy as np
import polars as pl
import scipy.ndimage
import scipy.stats
from functools import cached_property
from joblib import Parallel, delayed
from matplotlib.axes import Axes
from scipy.ndimage import gaussian_filter1d
from tqdm import tqdm
import stimpyp
from argclz import AbstractParser, argument
from ne... |
0ccfaf3d21ebd3ba64fd49fd5a13da69117834f481acc3438ec058031ab85a36 | Python | 11,665 | 358 | #!/usr/bin/env python3
"""
Fig4Sup2_CompetitionTitrations.py
Plots overlayed EC50 dose-response curves for GABA in competition with
various decoy ligands (1 mM fixed decoy concentration).
Usage:
python Fig4Sup2_CompetitionTitrations.py # Process all CSV/XLS files
python Fig4Sup2_Competition... |
0eb0e7f36fc460faee57e2cbeddb61cef52f83e8a3321a18e2547571ce54faff | Python | 11,669 | 360 | from __future__ import annotations
import json
import pytest
# Skip the whole module when the optional 'academy' extra is absent.
# Even though this file only touches the pure-stdlib parts of
# chemgraph.academy, the import guard is applied uniformly across the
# academy test suite so pytest collection stays clean o... |
5bee74bff890025b51b63720cf391700a83edb5fa93fbb797116a0e6e17700e9 | Python | 11,669 | 275 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
"""Module for building position mapping models based on pre-computed position tables"""
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import progressb... |
85528f73bd2a796d781f9fffcb663c82bc5cbb021731ad3efa688f415a2c5a5a | Python | 11,674 | 259 | import scipy.sparse, numpy as np, joblib, random, linecache, gzip, torch
from sklearn.ensemble import RandomForestClassifier
from sklearn.metrics import roc_curve, auc, average_precision_score, mean_squared_error, jaccard_score
# Given a set of files containing input feature data, determine which lines to read to defi... |
f71a39b0ea313058fbb5a1f0caf8691fefd78367abbcf8af873f7ee1d82f33af | Python | 11,676 | 379 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import io
import json
import mimetypes
import os
import shutil
from collections.abc import Sequence
from enum import Enum
from pathlib import Path
from typing import TYPE_CHECKING, Any
from PIL import Image
from ... |
0fb5e550d709a32e67ec125c9e435b2556229bfa278fbb9cb54626a43473c195 | Python | 11,686 | 255 | """(C) Copyright 2019 IBM Corp.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
d... |
404f6e018f76c6c1097d0c76b09a433eed9ee0790a36c76486bf438599aa320e | Python | 11,687 | 249 | import argparse
from os.path import join, isfile
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
import h5py
from model_zoo import lentiMPRA
import plotting
import pandas as pd
import wandb
from wandb.integration.keras import WandbMe... |
8ea5dcfcf6deade98647a1db68a1012dc35e5d74df72d405280071b603946137 | Python | 11,687 | 341 | # !/usr/bin/env python
# coding: utf-8
# @Time : 2022/9/23 13:25
# @Author : Z.-H. G.
# @Email_0 : guozhenhao17@mails.ucas.ac.cn
# @Email_1 : guozhenhao@tongji.edu.cn
# @File : preprocess_untils.py
# @IDE : PyCharm
import numpy as np
import pandas as pd
import scanpy as sc
import os
import logging
from typi... |
e89adcb0dc2843601cc692a3eace2065b1d30e7f99070dff7903f4f86b8b7759 | Python | 11,689 | 302 | """
Tests for `bx.align.maf`.
"""
from io import StringIO
from bx import align
from bx.align import maf
# A simple MAF from the rat paper days
test_maf = """##maf version=1 scoring=humor.v4
# humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
# /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.ma... |
683a6e2bec4e9e193f1f34f35b2498444bdaa949f179cf971d987ac56961cba3 | Python | 11,699 | 311 | import sys
sys.path.insert(0, '../')
sys.path.insert(0, '../../')
sys.path.insert(0, '../../../')
sys.path.insert(0, '../../../ogb')
import os
import argparse
import time
from shutil import copy
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
from ogb.linkproppred import PygLinkPr... |
7ec1f814c3dd3ab310ed478e77abbccead645c277cce98d7c003a549fbc139e9 | Python | 11,699 | 320 | from sklearn.model_selection import GridSearchCV
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import LabelEncoder, LabelBinarizer
from sklearn.metrics import accuracy_score, f1_score, roc_auc_score, confusion_matrix
from sklearn.svm import SVC
from sklearn.neighbors import KNeighborsClassifier
fr... |
459c41ba1bef5781774007e1c02a3dc4d7803b110809c894d429a2d3ed121692 | Python | 11,700 | 348 | # -*- coding: utf-8 -*-
"""
Implementation of various volumetric filter kernels
.. _FilterTypes:
Filter Type
-----------
Filter types defined by the ``ftype`` key include:
=============== =====================================
Type Descrition
=============== =====================================
``mean`... |
5cb0637b2d980698707e9c336413bf4576dbfa4461f66b001da03d8a22cead48 | Python | 11,700 | 317 | # -*- coding: utf-8 -*-
"""
This module defines the NormalizedWorm class
"""
import numpy as np
import pandas as pd
from collections import OrderedDict
import matplotlib.pylab as plt
from matplotlib import animation, patches
from .helper import DataPartition, nanunwrap
# i am including an excess of subdivisions wit... |
b365b391c91df87e2b7bde2eed7501e76bbb17e468f49cc4665b3a411da32f22 | Python | 11,704 | 308 | import numpy as np
import matplotlib.pyplot as plt
import tensorflow as tf
import os
import json
import cv2
import seaborn as sns
from matplotlib.colors import ListedColormap
from PIL import Image
import openslide
from typing import Tuple
import staintools
# Tensorflow Dependencies
import tensorflow as tf
from tensorf... |
e8c0f43c33a975f8595ddc3c603d07deeffe92b9182686384440e9698f9ae810 | Python | 11,705 | 374 | from __future__ import annotations
import os
import sys
import types
import warnings
from collections.abc import Callable
from collections.abc import Iterator
from pathlib import Path
from typing import cast
import pytest
from loguru import logger
from PySide6 import QtCore
from labelme.__main__ import _LOGGER_LEVEL... |
0299c299833e92c21d664c803ec5178f8b0e2e6403b2172a84e3492249f89c20 | Python | 11,708 | 303 |
from collections import defaultdict
import numpy as np
import pandas as pd
import anndata
from scipy import sparse
def binning(adata, bin_size=100, dim='3d', use_value='sum', celltype=None):
obs = adata.obs.copy()
obs['x_bin'] = (obs.x / bin_size).astype(int)
obs['y_bin'] = (obs.y / bin_size).astype(int)
... |
395eb18a1cc03754d00dcde45d8b1af829eaf79933769c23df3c5220843523dc | Python | 11,715 | 333 | import numpy as np
import polars as pl
from matplotlib import pyplot as plt
from matplotlib.axes import Axes
from typing import Literal, cast, get_args
from argclz import argument, AbstractParser
from neuralib.io import csv_header
from neuralib.plot import plot_figure
from neuralib.plot.colormap import get_customized_... |
38de1a9d45b291321aff01466126f01c6bce6674d84311a4d284a79b820d54f4 | Python | 11,720 | 378 | # 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.
"""
Wrapper around various loggers and progress bars (e.g., tqdm).
"""
import atexit
import json
import loggin... |
56670cfc828c8b4ae0ceeb01b7c7b0673f4b0c54543c74fe72cb4fa1a38e2401 | Python | 11,722 | 370 | import nibabel as nb
import numpy as np
import os
import glob
from nilearn import signal
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
ROOT = '/Users/sebastiandresbach/data/s1Anfunco/Nifti/derivatives'
# Set subjects to work on
subs = ['sub-05', 'sub-06', 'sub-07', 'sub-09', 'sub-10', 'su... |
fa2e285fde8d0a21ade21b4efb79d3d5a869eab2da99d988af5daaf8d2ff899d | Python | 11,723 | 253 | from ._extraction import *
from bread.data import Features, Segmentation, Lineage
import torch
if __name__ == '__main__':
import argparse
from pathlib import Path
from typing import List
from glob import glob
parser = argparse.ArgumentParser('bread.algo.lineage.nn.preprocess', description='extract training data ... |
61ec39239c20558f721b2df713980cf5ed88ccb46f14e60d74d7f491d1922959 | Python | 11,724 | 211 | import numpy as np
from src import utils, trnvaltst_sigmoid_oned, plot_figures
import tensorflow as tf
class EarlyStopping:
"""Early stops the training if validation loss doesn't improve after a given patience."""
def __init__(self, patience=7, verbose=False):
"""
Args:
patience (i... |
e273aacfb7ce8a190056402121a1d97bdc8a9fcf82e4396630768ed468fe28f7 | Python | 11,727 | 388 | #
# Copyright © 2009- The Spyder Development Team
# Copyright © 2014-2015 Colin Duquesnoy
#
# Licensed under the terms of the MIT License
# (see LICENSE.txt for details)
"""
**QtPy** is a shim over the various Python Qt bindings. It is used to write
Qt binding independent libraries or applications.
If one of the APIs... |
fe97a7976aa40cc795b65c063eb97b52ecb1061e882ed7622c79ab50d4079187 | Python | 11,731 | 322 | import warnings
from contextlib import nullcontext
from typing import Any, Dict, List, Optional
import torch
from torch import Tensor
try:
from transformers.tokenization_utils_base import BatchEncoding
except ImportError:
BatchEncoding = Dict
BOS = '<s>[INST]'
EOS_USER = '[/INST]'
EOS = '[/s]'
IGNORE_INDEX =... |
36d21a48d497c48d926f4f07ba454c97c77bbb4f4e8f2a38f32121ba27b389be | Python | 11,732 | 350 | from __future__ import annotations
import math
import pytest
from PySide6 import QtCore
from PySide6 import QtGui
from PySide6 import QtWidgets
from PySide6.QtCore import QPointF
from pytestqt.qtbot import QtBot
from labelme._utils._qt import _TintedSvgIconEngine
from labelme._utils._qt import direction_angle
from l... |
e4a08a6c005b836e4630897b5301684977b2a2fec010aa1aea2b1ed44236cb2a | Python | 11,732 | 367 | import torch.nn as nn
from .common import LayerNorm2d, UpSampleLayer, OpSequential
__all__ = ['rep_vit_m1', 'rep_vit_m2', 'rep_vit_m3', 'RepViT']
m1_cfgs = [
# k, t, c, SE, HS, s
[3, 2, 48, 1, 0, 1],
[3, 2, 48, 0, 0, 1],
[3, 2, 48, 0, 0, 1],
[3, 2, 96, 0, 0, 2],
[3, 2, 96, 1, 0, 1],
[3, 2,... |
985052e46ef83b3f67e28d01aaec2b85691dd07941a07f163d0763378993a1e3 | Python | 11,740 | 332 | # 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, ... |
bb1a4029a2e77ff8a38934570dea744e2265b063b8a412149b7d577c97f46821 | Python | 11,740 | 389 | import re
import io
import sys
import time
import zlib
import json
import shutil
import typing
import struct
import pickle
import pathlib
import argparse
import threading
import traceback
import itertools
import contextlib
import subprocess
import collections
from multiprocessing.pool import ThreadPool
import yaml
imp... |
5c3a4abdebe8d365c9ef5789d1edff3e6d4630771cbfd87466cc639f3fad9066 | Python | 11,741 | 330 | # custom_pinn_utils.py
import numpy as np
import tensorflow as tf
from deepxde import optimizers, config
from deepxde.nn import activations, initializers, regularizers
from deepxde.display import TrainingDisplay
from deepxde import Model, config, optimizers
from deepxde.nn import regularizers, activations, initializer... |
a0f38253f2ea845d12affb849c39be0c92e63f34b2d505ac106f9c9e10af2f83 | Python | 11,741 | 246 | #!/usr/bin/env python3
"""Create, inspect, upload and publish a checked Zenodo software release.
Uses Zenodo's current InvenioRDM API. Credentials are read from a mode-0600
file and are never printed. Destructive publication is a separate subcommand
that revalidates the draft, archive checksum, record ID and reserved ... |
09af0c9f4ee028f3b46de7f5b1864a42405e7dcc58d54b1cc39d0325caca3546 | Python | 11,743 | 234 | #!/usr/bin/env python
# This is a pipeline doing resting-state fMRI preprocessing as done in the PAINTeR study
# https://github.com/spisakt/PAINTeR
#
# The pipeline performs:
# - a standard anatomical image processing (AnatProc) with:
# - brain extraction with FSL bet
# - FSL FAST tissue segmentation
# - ANTs-bas... |
d7cd3efd1098dd934c509ffd8e35da7e7d9f4937cb4dead4d46c0f748077430d | Python | 11,743 | 197 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'film.ui'
#
# Created by: PyQt5 UI code generator 5.7
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_GroupBox(object):
def setupUi(self, GroupBox):
GroupBox.setObject... |
1904fb72e5d7035450a8c5afbdc249ad057a24b3e4d363d0d48677568b4b5a2e | Python | 11,745 | 349 | """residual attention network in pytorch
[1] Fei Wang, Mengqing Jiang, Chen Qian, Shuo Yang, Cheng Li, Honggang Zhang, Xiaogang Wang, Xiaoou Tang
Residual Attention Network for Image Classification
https://arxiv.org/abs/1704.06904
"""
import torch.nn as nn
import torch.nn.functional as F
#"""The Attentio... |
056c391a02bb282ed33a134ad9c509e58a06cbfd03bfa0c2fcdbb04126a756b7 | Python | 11,749 | 250 | # Loss functions
import torch
import torch.nn as nn
from utils.general import bbox_iou
from utils.torch_utils import is_parallel
def smooth_BCE(eps=0.1): # https://github.com/ultralytics/yolov3/issues/238#issuecomment-598028441
# return positive, negative label smoothing BCE targets
return 1.0 - 0.5 * eps,... |
9ea1882e5dcc44a8ba43484291c442554c157b0f7243838d5d034cc95712244f | Python | 11,752 | 249 | import torch
import numpy as np
from torch.nn import functional as F
class ResNet2D_block(torch.nn.Module):
def __init__(self, channels=128, rate=1):
super(ResNet2D_block, self).__init__()
self.inorm1 = torch.nn.InstanceNorm2d(num_features=channels, eps=1e-6, affine=True)
self.inorm2 = torc... |
15f254108896a10fc65e46debfb361613ae7df6058aec531f9c83b4cd090926a | Python | 11,753 | 245 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Agatha Schmidt, Henrik Zunker
#
# 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 complian... |
8fea771926f5dec0ac76d6919149d261c0b16ba62bf520d7d1241ffb02ef9fa6 | Python | 11,755 | 267 | import warnings
from collections.abc import Callable
from typing import Any, cast
import torch
from eir.train_utils.ignite_port.engine import Engine
from eir.train_utils.ignite_port.events import Events
from eir.train_utils.ignite_port.metrics.metric import (
Metric,
MetricUsage,
RunningBatchWise,
Sin... |
cce8954c0b53c9c3aa3fdc56a667910a9c0179d2d1d6f292abe4cde8d99d599b | Python | 11,757 | 334 | # -*- coding: utf-8 -*-
#
# LightGBM documentation build configuration file, created by
# sphinx-quickstart on Thu May 4 14:30:58 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... |
70967f040256b5864c360f4c5e18c35e8b4eb7428281bd3e06bf2462c0360922 | Python | 11,758 | 401 | #!/usr/bin/env python
#import sys
import numpy as np
#from scipy import optimize
import matplotlib
import matplotlib.pyplot as plt
import os
import argparse
from datetime import datetime
import csv
import glob
import itertools
from matplotlib import ticker
import sys
matplotlib.use('agg') # Gets rid of GUI dependenc... |
8eb29034cabf8bebe356ec040446cf6d09efcd323c4bf13848b218e49f68adff | Python | 11,759 | 293 | import os
import glob
import tqdm
import json
import numpy as np
import matplotlib.pyplot as plt
from collections import Counter
############################################################################################################################################
DATA_DIR = r"D:\Askivit Daten\ASKIVIT_... |
cee071068924d962c6442c02668eb34b1490c6ac7598a5c2b433810c1001a71b | Python | 11,760 | 289 | # Kai Sandbrink
# 2023-02-14
# This script analyzes the mistrained model
# %% LIBRARY IMPORTS
import torch
import numpy as np
import os, copy
import pickle
import matplotlib.pyplot as plt
from utils import Config, plot_learning_curve, get_timestamp
from ObserveBetEfficacyTask import ObserveBetEfficacyTask
from PeekTa... |
e744cd2028c39f2f5db000b27719e7feb61df3d41c03ef900c42c8332a931545 | Python | 11,764 | 281 | from collections import defaultdict
from typing import Set, Tuple, List
import networkx as nx
from networkx import DiGraph
from zigzag.classes.hardware.architecture.memory_instance import MemoryInstance
from zigzag.classes.hardware.architecture.memory_level import MemoryLevel
from zigzag.classes.hardware.architecture.... |
0d6679450fe1d82ed9d7eb0814ff593bc7d74620637e570e32d67bd943992bfe | Python | 11,769 | 270 | '''Tests for Attributors.'''
from functools import partial
from itertools import product
import pytest
import torch
from zennit.attribution import Gradient, IntegratedGradients, SmoothGrad, Occlusion, occlude_independent
class IdentityLogger(torch.nn.Module):
'''Helper-Module to log input tensors.'''
def __... |
afe7960359a251d0efd9b1c91791cca2f92ffd04ce1ea51ae3d271df07280f5c | Python | 11,770 | 270 | import torch
import torch.nn as nn
import spikingjelly.activation_based.layer as layer
from copy import deepcopy
from spikingjelly.activation_based import neuron, surrogate
import torch.cuda.nvtx as nvtx
def conv3x3(in_planes, out_planes, stride=1, groups=1, dilation=1):
"""3x3 convolution with padding"""
retu... |
ea726c5ea73830e52fc4f0ed14c1238b1b82ea4bfe0e3e0258f90be803fffab8 | Python | 11,770 | 304 | """
HMM: Plotting MEG Networks
==========================
In this tutorial we will plot networks from an HMM trained on source reconstructed MEG data. This tutorial covers:
1. Load multitaper spectra
2. PSDs
3. Power maps
4. Coherence networks
5. Coherence maps
6. Coherence vs Power
"""
#%%
# Download post-hoc spect... |
ca72341e1d574bd73edcc2f62b8dd261b305d2bdb89ece483217b9f74c45ca13 | Python | 11,773 | 315 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_scatter import scatter
from torch_geometric.nn import InstanceNorm
class EGNNLayer(nn.Module):
"""
EGNN layer with optional feed forward network and batch normalization.
Args:
input_nf: Number of input node features
... |
7fe450960c409f90f2bd1327214eab4730bff3a5d640b871a6c02d079b8dd887 | Python | 11,774 | 327 | from __future__ import annotations
from collections.abc import Iterator
from typing import Final
from typing import NamedTuple
from typing import cast
from PySide6 import QtCore
from PySide6 import QtGui
from PySide6 import QtWidgets
from PySide6.QtCore import Qt
from PySide6.QtWidgets import QStyle
from .._shape im... |
369fa88d129c506a4e55bccd8d322d1266b250a47bbb2668d5879928ecab7f2c | Python | 11,775 | 275 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import math
from collections.abc import Generator
from itertools import product
from typing import Any
import numpy as np
import torch
def is_box_near_crop_edge(
boxes: torch.Tensor, crop_box: list[int], orig... |
f10816c6dbbf2ed613e8f678ee0420f381c89094b16fa88ce6ae920aa11e9116 | Python | 11,779 | 325 | # type: ignore # This file is adapted from external source and kept untyped
"""
Adapted from: https://github.com/Blealtan/efficient-kan/blob/master/src/efficient_kan/kan.py
Original Author: Blealtan and akaashdash (Efficient KAN repository)
Notes: This version may include modifications. KANs require flattened input sh... |
3b2ffadb8f29eb2adff2a926104a9b8205995e1e364b4350ccb743e16aefcc12 | Python | 11,783 | 350 | from __future__ import annotations
import asyncio
import dataclasses
import json
from pathlib import Path
from typing import Any
import pytest
# Skip when the optional 'academy' extra is absent.
pytest.importorskip("academy")
from chemgraph.academy.core import agent as agent_module
from chemgraph.academy.core impor... |
bf136583d938ccf2f6eab349b7ccafd5222767520264150eb65e1bcb7155b9ef | Python | 11,785 | 369 | from collections.abc import Generator, Sequence
from dataclasses import asdict, dataclass, fields
from pathlib import Path
from typing import Optional
import numpy as np
import torch
from PIL import Image
from timm.models._registry import _model_pretrained_cfgs
from torchvision import transforms
from torchvision.trans... |
782005e9948bb63bb8daf825073ddb493f4fb6a2b8905d030bfa68159639c3d0 | Python | 11,786 | 232 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '/media/lg/disk2/PycharmProjects/ISAT_with_segment_anything/ISAT/ui/model_manager_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 ed... |
8ae6ed0517f3d6daf596b3d078a5299faa791c49525ec3c2b7cd988220275c1b | Python | 11,790 | 250 | '''
embeddings::glove.py
Wrapper functions to transform, load and sample GloVe.
Available as embeddings.glove.*
'''
from .internal import *
import os
import numpy as np
from sklearn.decomposition import PCA
from gensim.models.keyedvectors import KeyedVectors
from gensim.scripts.glove2word2vec import glove... |
fb427c5281a1204ef9d9a0220dc09a08d6362fcb93862fc4798cd87d1aececc2 | Python | 11,793 | 303 | import torch
from torch import nn
from torch.nn import functional as F
from torch.nn import init
from .pooling import build_pooling_layer
class SeparableConv2d(nn.Module):
def __init__(self,in_channels,out_channels,kernel_size=1,stride=1,padding=0,groups =1, dilation=1,bias=False):
super(SeparableConv2d,se... |
d5beb053ee984ee2ec5a7e69f1ce4b5d09b62ae8040157046092996d64c3be04 | Python | 11,796 | 315 | import copy
from typing import Any, List, Optional, Union
import numpy as np
import torch
from torch import Tensor
import torch_geometric.typing
from torch_geometric.typing import Adj
class InvertibleFunction(torch.autograd.Function):
r"""An invertible autograd function. This allows for automatic
backpropag... |
8f5780e101fc5d08b8c21b058bb8bb6477232a050d735dd1ca04c7a76b5e8ce6 | Python | 11,801 | 325 | import numpy as np
import torch
from torch import Tensor
from typing import Tuple, List, Dict
__all__ = [
'rel_location2abs_location', 'filter_contours_by_stitching_rule', 'fouriers2contours', 'get_scale', 'scale_fourier',
'scale_contours', 'batched_box_nms', 'batched_box_nmsi', 'order_weighting', 'remove_bord... |
cd53cd4303f34849758ce76bca6c3b1914679cffaac5d81dc9fd80c597316d4e | Python | 11,804 | 160 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '/media/lg/disk2/PycharmProjects/ISAT_with_segment_anything/ISAT/ui/remote_sam_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 edit ... |
f27bf6268ca0e0a2b002bd1e464cedf5548275bc967808df19e09568fee75175 | Python | 11,805 | 217 | #!/usr/bin/env python3
# Copyright (c) 2022, Hyewon Jeong, 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 distr... |
a8b89212678f4780d7d1bd202589e37260ac302eb4781b9b60a0f2fd49ddf54b | Python | 11,806 | 281 | # -*- coding: utf-8 -*-
"""
Created on Wed Mar 10 15:01:03 2021
@author: mtodorov, adapted by Julian McGinnis
"""
import numpy as np
import csv
import nibabel as nib
from tqdm import tqdm
import pandas as pd
import datetime
import argparse
from xml.etree import ElementTree as ET
import io
parser = arg... |
453b5e4d8c8e43e08136645b524d42544393e1e419bcf04f233ac4f3bb7bda0d | Python | 11,807 | 264 | """
Decompose graph generation and embedding generation
Embedding generation is gpu bounded while graph generation is cpu bounded
Improve the edge distance computation via torch.cdist
"""
import os, random, re, sys
sys.path.append('..')
from pathlib import Path
import math
import warnings
warnings.filterwarnings("ignor... |
d28e0974ebd0c74ccf717c031ac5c50d0f6131b6cf53a634d1048d8d3ec466d6 | Python | 11,808 | 315 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 30 20:56:17 2016
@author: ajaver
"""
import json
import numpy as np
import pandas as pd
import tables
from scipy.interpolate import interp1d
from scipy.ndimage.filters import median_filter
from scipy.signal import savgol_filter
from tierpsy.analys... |
a7894e609a1f2662bb4c2eceae1adfd992b483613056176a28f19577cbef0a1e | Python | 11,813 | 337 | """Simplified preprocessor and Dataset for SOTA datasets."""
import os
from typing import Any
import numpy as np
import pandas as pd
import torch
from torch.utils.data import Dataset
from mcmlnet.experiments.data_loaders.simulation import ManojlovicSimulationLoader
from mcmlnet.utils.env import require_env
from mcml... |
8c913f67bea2cfb11c0e3c028c2377b9a72a2ffb2a124c67426abc8f723568db | Python | 11,814 | 344 | #!/usr/bin/env python
import numpy as np
from vtk.util import numpy_support
from xml.etree.ElementTree import ElementTree
from collections import namedtuple
class vtuWriter:
"""
USAGE:
vtk_writer = vtuWriter()
vtk_writer.writeVTU("filename.vtu", pts, all other optional arguments...)
vtk_writer.wr... |
3f10ab5708819636c96dc55d79e1b3403d5818e2e4c90c0462044398e1807e50 | Python | 11,816 | 299 | import os
import glob
import torch
import torch.optim as optim
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import torch as tc
import nibabel as nib
from model import ModelWrapper
import random
import math
import monai
from monai.data import DataLoader
from monai.transforms import Compose, Load... |
79cecf156c9e3c0a8885ea8b1431e59d965146c4413499b13eafd768ff14b355 | Python | 11,817 | 296 | """Tests for hypnogram upsampling: hypno_fit_to_data and Hypnogram.upsample_to_data.
Covers all combinations of:
- data type : NumPy array | MNE Raw without meas_date | MNE Raw with meas_date
- Hypnogram : no start | naive start | tz-aware start (via tz=) | tz-aware datetime
Default behaviour (meas_date_is_local=... |
89f98458e4a5c1f6c81b26ed3678ce60a7b56df4736f669ae118c333506a3ad1 | Python | 11,820 | 292 | # Imports
import sys
import os
import pandas as pd
import numpy as np
import random
from scipy.integrate import odeint, solve_ivp
from lmfit import minimize, Parameter, Parameters, report_fit
from model_functions_loco_Rew1 import *
import matplotlib.pyplot as plt
from pathlib import Path
########## DATA LOAD ########... |
4b2aa453c55977b01a26eb12a5f87deea02493506438f7ee965bc58956a1d35d | Python | 11,831 | 351 | """
Pipeline for VTK filters.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from .decorators import wrap_input
from .wrappers.algorithm import BSAlgorithm
from .wrappers.data_object import BSDataObject
# From https://vtk.org/Wiki/VTK/Tutorials/New_Pipeline
# Outputs are referred... |
c1260e9f61d3f1b682dcae8f7ca3a9f6f30214782fb6e2e956c0c24778bf3965 | Python | 11,832 | 416 | from unittest.mock import MagicMock
import pytest
import torch
from torch import nn
from eir.train_utils.optim import _get_all_params_to_optimize, get_optimizer
@pytest.fixture
def create_test_model():
class TestModel(nn.Module):
def __init__(self):
super().__init__()
self.fc1 = ... |
e3500ee22e56f0e508357d1008852549d0222f3fdd1197a0e551cb7e5a181141 | Python | 11,833 | 438 | from __future__ import print_function
import argparse
import os
import sys
import subprocess
import pandas
import gzip
import glob
import re
PIPELINE_PATH = os.path.join(
os.path.abspath(os.path.dirname(__file__)),
)
chr_pattern = re.compile(r'chr(\w+)\..+')
# def filetype(arg):
# if os.path.isfile(arg):
# ... |
4144f6e09a3152be6f20c5a4bce6b3359279d8af21341b456f09d5381973a8d6 | Python | 11,836 | 331 | import gc
import os
import pickle
import numpy as np
import pandas as pd
import torch
from scipy.stats import spearmanr
from sklearn.metrics import r2_score
from SWOW_prediction.data_preprocessing import construct_property_dataset
from SWOW_prediction.loss import get_l1_regularization, get_likelihood_loss
from SWOW_p... |
e2d6e733d64ea41e50618e333cac6a976352f852dda155137b6dff410a58eebe | Python | 11,840 | 303 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# MRC CBU PYTHON SCANNING SYNC
#
# This library is intended to allow for easy communication between Python
# experiments and the MEG and MRI scanners at the MRC Cognition and Brain
# Sciences Unit (CBU). The implementation is intended for the CBU setup only,
# and interf... |
28094c10dac371b89149f93cce477d0cb7f850cdbd566a4a4e04fa9dd8f33449 | Python | 11,841 | 330 | from Bio.PDB import PDBParser, MMCIFParser, NeighborSearch, Selection
import subprocess
from pathlib import Path
import sys
MODULE_DIR = str( Path( Path(__file__).parent.resolve() ) )
sys.path.append(MODULE_DIR)
AA3to1_DICT = {'ALA': 'A', 'CYS': 'C', 'ASP': 'D', 'GLU': 'E', 'PHE': 'F', 'GLY': 'G', 'HIS': 'H', 'ILE': '... |
9421760a05514d1800f5eb1604d5827943558ab42e9b6fde457e24c0380b7bd3 | Python | 11,841 | 346 | """Provider-independent discovery, native tool execution, and turn isolation."""
import json
import sys
from types import ModuleType
import pytest
from langchain_core.messages import AIMessage, HumanMessage
from langchain_core.tools import tool
from langchain_core.utils.function_calling import convert_to_openai_tool
... |
e5c430db7af53255cdf8e9cc2ce3e045d808aa92152413b46dbb7d051f2b88f1 | Python | 11,845 | 352 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""
COCO prediction dumper for distributed training.
Handles collection and dumping of COCO-format predictions from models.
Supports distributed processing with multiple GPUs/processes.
"""
import copy
import gc
import heapq
import json
import ... |
11e52cddf32be47cdf1d148934de083c248b1c5b9e4cc9b068df53ba00e4d4ad | Python | 11,846 | 291 | # flake8: noqa
import os
import numpy as np
from scipy.optimize import linear_sum_assignment
from .. import _timing
from ._base_metric import _BaseMetric
class HOTA(_BaseMetric):
"""Class which implements the HOTA metrics.
See: https://link.springer.com/article/10.1007/s11263-020-01375-2
"""
def _... |
8a029448bdb553ca5a3a6c2f1a77d44e401554b6205a3077e52403e249bd7f70 | Python | 11,846 | 270 | # 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 numpy as np
import torch
from .modeling import Sam
from typing import Optional, Tuple
from .utils.transforms imp... |
f8bd377ead1506f06c14e9b1ebe1fa60033a05ab6db5bfd972a44f4378fec038 | Python | 11,848 | 338 | import logging
from typing import List, OrderedDict
import numpy as np
import torch
from scvi import _CONSTANTS
from scvi._compat import Literal
from scvi.distributions import NegativeBinomial
from scvi.module import MRDeconv
from scvi.module.base import BaseModuleClass, LossRecorder, auto_move_data
from scvi.nn impor... |
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