sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
506e622e7e67a301bc16f8cde4670bb0ed5493109d8f8581bbee8b14c65c181c | Python | 9,397 | 229 | import schnetpack as spk
import readline
import os
from sys import argv
import numpy as np
from ase import Atoms
from ase.units import Bohr
from schnetpack.data import AtomsData
def read_dataset(path,numberofgeoms,filename):
atom_buffer = []
property_buffer = []
charge_buffer = []
metadata = {}
for... |
db3ad2eeb76eece7b6d78df1b260a577c1fad486d2a709ebbbd1837920902db6 | Python | 9,397 | 291 | """distutils.core
The only module that needs to be imported to use the Distutils; provides
the 'setup' function (which is to be called from the setup script). Also
indirectly provides the Distribution and Command classes, although they are
really defined in distutils.dist and distutils.cmd.
"""
import os
import sys
... |
fd8549afe00f1a92e3e728ce1b5df15388cb68871adb575b83009d431a73f148 | Python | 9,397 | 263 | import numpy as np
from torchvision.models.resnet import Bottleneck
from wsilearn.utils.cool_utils import *
from wsilearn.dl.np_normalizer import create_input_normalizer
from wsilearn.dl.models.model_internal_utils import ModelHook
from wsilearn.dl.np_transforms import NumpyToTensor
from wsilearn.dl.torch_utils import... |
37bfa489072d523fbcb29b793e2b9af21fc9e65791da3ca12624e5cb7b510a9a | Python | 9,399 | 240 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
8e31634aa35fed6dbe4dae98524cb02b43f87768b4073fcca8b39f97b3b54e4c | Python | 9,399 | 328 | """Handwritten parser of dependency specifiers.
The docstring for each __parse_* function contains ENBF-inspired grammar representing
the implementation.
"""
import ast
from typing import Any, List, NamedTuple, Optional, Tuple, Union
from ._tokenizer import DEFAULT_RULES, Tokenizer
class Node:
def __init__(sel... |
50b7b4a78a86674cf42a33e74cd74aacaf9b6b7d7fadb7c3838b086cb8da89fc | Python | 9,402 | 229 | import schnetpack as spk
import readline
import os
from sys import argv
import numpy as np
from ase import Atoms
from ase.units import Bohr
from schnetpack.data import AtomsData
def read_dataset(path,numberofgeoms,filename):
atom_buffer = []
property_buffer = []
charge_buffer = []
metadata = {}
for... |
ac4ea7d123694ba9cd5b1f04f0c36deaf5a998afe5a7c778170a266bb26f2b82 | Python | 9,402 | 281 | from __future__ import annotations
import os
from importlib.util import find_spec
from pathlib import Path
import pytest
from ase import units
from ase.io import read
from pymatgen.io.qchem.inputs import QCInput
from quacc.calculators.qchem import QChem
has_obabel = bool(find_spec("openbabel"))
FILE_DIR = Path(__f... |
e173adab2bd40a5a74c2933e926edc3917049a06a5a2b92bc2f39fc982206e59 | Python | 9,409 | 335 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
7a19a1fd089bce5d8918f96dfbee7802eb6e64addb1386f8536c558d27b76ec3 | Python | 9,413 | 221 | from pathlib import Path
from collections import defaultdict
import numpy as np
import pandas as pd
from pathlib import Path
from tqdm import tqdm
import pandas as pd
from torch.utils.data import DataLoader
from wsilearn.utils.cool_utils import read_json_dict, mkdir, Timer, is_string_or_path
from wsilearn.datacon... |
e47b81723df0b8d9fa810786ff5c924380e18d9cb270f1989658deaf81c93eb0 | Python | 9,418 | 317 | # pylint: disable=invalid-name, missing-function-docstring, missing-class-docstring, unused-argument, too-few-public-methods, no-member, too-many-arguments, line-too-long, too-many-instance-attributes
""" FBNetGen model sub-modules from https://github.com/Wayfear/BrainNetworkTransformer"""
import time
import numpy as... |
a0fff19bd588fdf24b9d0a14314546ed6b771bcf6725953f744af030717cfbfa | Python | 9,420 | 218 | from pathlib import Path
import natsort
import numpy as np
import PIL.Image
import matplotlib.pyplot as plt
import pandas as pd
import cv2
import glob
import os
import re
import Dicts
def get_cts(patient, use='mod', w='1', mods='gaussian'):
path = ''
if use == 'original':
path = r"../../data/output_da... |
f8fadc009d01447222c15ff323560e99a65839408fda2325b6da3d94af260c26 | Python | 9,421 | 243 | #!/usr/bin/env python
"""
Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later ver... |
33cd79e0ccf5a1bf63a9cd2b4c6554e77030aaf971d6cd385781f45f90e1cf2f | Python | 9,422 | 253 | # Script to perform polynomial regressions on TVAT data
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nhost = comm.Get_size()
except ModuleNotFoundError:
rank = 0
nhost = 1
from os.path import join
from get_paths import *
import h5py
import numpy as np
import matplo... |
4ac3fc3f776eee7358d125ed13c39b4ed66d690eee8b570bfc77b55807cefbed | Python | 9,428 | 220 | ''' Script to run and plot stats on sensor-level decoding patterns.
Cluster based permutations in space and time are used.'''
proj_name = 'MINDLAB2020_MEG-AuditoryPatternRecognition'
import sys
sys.path.append('/projects/' + proj_name + '/scripts/working_memory/')
import mne
import numpy as np
from matplotlib import ... |
79a4c5fae2196fa7a2db30ee8cc3f744e743fc87562bb809c8dd18ba53018684 | Python | 9,430 | 313 | #!/usr/bin/env/python
# Copyright (c) Facebook, Inc. and its 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 collections import defaultdict
import os
import pickle
import json
import torch.nn as nn
import ... |
dbdbadbc0a136734b01415dbf371b516198efecb11430e5722b72fda9d3cc973 | Python | 9,431 | 273 | from __future__ import annotations
import os.path
import re
import shutil
import tempfile
import zipfile
from glob import iglob
from ..bdist_wheel import bdist_wheel
from ..wheelfile import WheelFile
from . import WheelError
try:
from setuptools import Distribution
except ImportError:
from distutils.dist imp... |
f60b6b5a4fa2b753c7320990b173cfe39e79d9ea4504ebae56fd4b5e76b151fe | Python | 9,431 | 237 | from argparse import ArgumentParser
import ast
import pytorch_lightning as pl
import torch
import os
import torch.nn as nn
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' # tf warnings set to silent in terminal
from pytorch_lightning.callbacks import ModelCheckpoint
from torchvision.models import resnet18, resnet34
from mode... |
86243744c39c1be0a6ed30e620822a95aa4cfb6e29834cf19774ebae68136036 | Python | 9,433 | 179 | # Want to take 50% of task evoked and resting state trials (resting state trials are dummy)
# Want to compute CCA for both
# Want to store evoked time course of component 1
# Repeat 1000 times
# Get correlation between time courses - should be higher for task evoked versus resting state
import numpy as np
import panda... |
b7ab9ad0bd82524fe2bf3564ece7541ad5ca1c3a7d2f3546d5490fbbde1c29a5 | Python | 9,433 | 260 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# 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,... |
1d01b88d1b6a9e425cb9147ecfb604598825a7df2e8bbaab98b38f90e2f76b03 | Python | 9,435 | 275 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
029b04b3de15f1c923d91ca84748a4463a162208ed6b466f019757f5de3b3c8f | Python | 9,437 | 303 | # pylint: disable=invalid-name, missing-function-docstring, missing-class-docstring, unused-argument, too-few-public-methods, no-member, too-many-arguments, line-too-long, too-many-instance-attributes, too-many-locals
""" MILC model module from https://github.com/UsmanMahmood27/MILC"""
from copy import deepcopy
impor... |
96ae6a314876f458c49a08be98012f0e4400d65df9b3b0f7ce8ff974fb56451e | Python | 9,437 | 244 | """
Created on 29/06/2020
:author: Chinchien Lin
:summary:
"""
import sys
import SimpleITK as SITK
import json
import datetime
import os
from src.utils import sitk_utils as sutils
class RegistrationFromMaps:
"""
Perform map-based registration using the pre-generated transformation parameter f... |
d3f9cd76add69b04906cec484265ea656480ae81f2714dba6636011f25a8927a | Python | 9,437 | 248 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : micro_env_features.py
# Author : Yufeng Liu
# Date : 2023-01-18
# Description :
#
#============... |
666b78c0c02d5d96cb7155f22907a4277f2701eb844dbfdc137da45a390b7901 | Python | 9,438 | 307 | from __future__ import print_function, division, absolute_import
import torch
import torch.nn as nn
import os
import sys
class BasicConv2d(nn.Module):
def __init__(self, in_planes, out_planes, kernel_size, stride, padding=0):
super(BasicConv2d, self).__init__()
self.conv = nn.Conv2d(in_planes, ou... |
c42045472e7ea6ab81e4135e41c1f54edb641ba9c9f3b426041e61a0c17a462f | Python | 9,442 | 230 | from typing import List
from typing import Union
import numpy as np
from skimage import transform
from skimage import feature
from skimage import registration
import cv2
from merlin.core import analysistask
from merlin.util import aberration
from merlin.util import imagewriter
class Warp(analysistask.ParallelAnalysis... |
10b34161adfe67b682eb30cc043256aaff79c9b87b394db7401c27254f753477 | Python | 9,443 | 292 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
2f1444827aa2805519d619f4a7508a4b6b4f45df3dec9fd92e37585e8a564585 | Python | 9,443 | 313 | import os
import argparse
import torch
from sklearn.metrics import roc_auc_score
import numpy as np
from maldi_nn.models import AMRModel
from maldi_nn.utils.data import DRIAMSAMRDataModule
from lightning.pytorch.callbacks import ModelCheckpoint, EarlyStopping
from lightning.pytorch.loggers import TensorBoardLogger
from... |
4fa78504a699858c7422e957c4a067d5e3bd4515c41eff133f4cf09241c0bd74 | Python | 9,443 | 267 | '''
This code is modefied based on a TCN impelemtation by https://github.com/locuslab/TCN
'''
import os
import csv
import math
import joblib
import argparse
import numpy as np
from pathlib import Path
from scipy.stats import pearsonr, spearmanr
import torch
import torch_xla
import torch_xla.core.xla_model as xm
impor... |
aabb948eb314dd41aad02f8c724bcd02807ccd41445c0c66cba7ca044b723d9a | Python | 9,445 | 246 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
61dcb2735817c1a34fc396785f487b27f7b0e7c7002b987508fa1290d1426d41 | Python | 9,446 | 250 | """Wrapper for converting a Meep simulation into a differentiable JAX callable function.
Usage example:
```
import jax.numpy as jnp
import meep as mp
import meep.adjoint as mpa
sources = [
mp.EigenModeSource(...)
]
monitors = [
mpa.EigenmodeCoefficient(...),
mpa.EigenmodeCoefficient(...),
]
design_regions = [... |
b91764361f685f2e86dc765f8875e2944c67659d34711a2376ef8a81dc9459e1 | Python | 9,446 | 233 | import numpy as np
import sys
from pydrake.all import (
BasicVector,
LeafSystem,
PortDataType,
)
from pydrake.util.eigen_geometry import Isometry3
from pydrake.trajectories import (
PiecewisePolynomial
)
from pydrake.math import RollPitchYaw
from robot_plans import *
class ManipStationPlanRunner(Lea... |
f9aece5b33622d1836f5611d1e9aa8114245dca3d034b03dbc7b0d647b752d12 | Python | 9,446 | 262 |
"""
Created on Fri Jul 17 16:59:51 2020
@author: Leonardo Bonetti, Francesco Carlomagno
leonardo.bonetti@clin.au.dk
"""
#To use this script please do the following:
#-place the provided stimuli folders in your favorite directory
#-assign to the variable 'stimidr' (few lines below) such directory
#-define your log ... |
3634263fd35b82ecf7ad4426d993d3cae1edaacb4bd8bcb558311886699e9bd8 | Python | 9,449 | 349 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
6226d4cece5f33a72a038b2bad7afa6ed6df26ed0f3dc2cbf1e0de6fed3da427 | Python | 9,450 | 312 | #adapted from: Pingjun Chen
# https://github.com/PingjunChen/tissueloc/blob/master/tissueloc/locate_tissue.py
# MIT License Copyright (c) 2018 Pingjun Chen
## Changes: output asap tif masks, support for spacing parameter
## Note: fat is sometimes not recognized
import argparse
import sys
from pathlib import Path
fro... |
639632a2d6a7912e8c894b1244f2cc791a1cffc843a1ee8eef2960f8daa5ddb0 | Python | 9,450 | 310 | # -*- coding: utf-8 -*-
#
# syncopy.connectivity backend method tests
#
import numpy as np
import matplotlib.pyplot as ppl
from syncopy import synthdata
from syncopy.connectivity import csd
from syncopy.connectivity import ST_compRoutines as stCR
from syncopy.connectivity.wilson_sf import wilson_sf, regularize_csd, ma... |
ebba0eb5d0c626444479c80a9308052a13669f9478f5ef4be958cd301661d2c4 | Python | 9,451 | 275 | """Test the full PREP pipeline."""
import matplotlib.pyplot as plt
import mne
import numpy as np
import pytest
import scipy.io as sio
from pyprep.prep_pipeline import PrepPipeline
from .conftest import make_random_mne_object
@pytest.mark.usefixtures("raw", "montage")
def test_prep_pipeline(raw, montage):
"""Tes... |
c8ac7b8b3a8d877a69b6250031fee609f1dde78df272aeb45a4344d21639ae19 | Python | 9,452 | 339 | """
=============
Preprocessing
==============
Extracts relevant data and removes artefacts.
Authors: José C. García Alanis <alanis.jcg@gmail.com>
License: BSD (3-clause)
"""
# %%
# imports
import sys
import os
import warnings
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
from mne i... |
f82c1603dc9e354d9798b7645b6657c105f1b01ea9ba614776a29c1495e3ba8e | Python | 9,454 | 197 | from argparse import ArgumentParser, Namespace, FileType
from Bio.PDB import PDBParser,MMCIFParser
from Bio.PDB import PDBIO, MMCIFIO, Select
import os,copy
from tqdm import tqdm
from utils.relax import openmm_relax, openmm_relax_protein_only
from rdkit.Chem.rdmolfiles import MolToPDBBlock, MolToPDBFile
import rdkit.C... |
3b7651c91a754a9ed6ccdd67b071d0648945b4905e1e4e145cbe4591d1c3b949 | Python | 9,455 | 153 | """
Builds the database in two main steps:
1) Imports all the data from ontologies, databases and experiments
2) Loads these data into the database
The module can perform full updates, executing both steps for all the ontologies,
databases and experiments or a partial update. Partial updates can e... |
b2ff812956e07156b2f66dfd1c580ddfa12dd9fceab7d95614396a3ff79293fd | Python | 9,456 | 289 | from collections.abc import Callable, Iterator
from pathlib import Path
import cocotb as ctb
import pytest
from cocotb.clock import Clock
from cocotb.triggers import RisingEdge
from cocotb.types import LogicArray
import elasticai.creator.function_dispatch as FD
import elasticai.creator.ir as ir
from elasticai.creator... |
e72ed2899a96bb6d387cb774a49fadd708df4906e2fc1478273188d8f3ec5732 | Python | 9,456 | 210 | from __future__ import print_function
import argparse
import os
# os.environ['KMP_DUPLICATE_LIB_OK'] = 'True' # this code is for windows platforms
import sys
from AdaHB import Adaptive_HB
from PIDAO_SI_AAdRMS import PIDAccOptimizer_SI_AAdRMS
from PIDopt import PIDOptimizer
from PIDAO_SI import PIDAccOptimizer_SI
proje... |
13a31861a1ed1246d2a7a3e8401718594b21a0ce87daefe8a7660f7d3b8b0181 | Python | 9,457 | 213 | """
creates a methylation plot over a given cohort
"""
import sys
import seaborn as sns
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import argparse
import os.path
def parse_args():
parser = argparse.ArgumentParser(description="Script to create a met... |
5d8f922aaf51937e77e2fe828af0622028e28d8b2823bdf3f14286df8d316ff2 | Python | 9,459 | 214 | from typing import List, Union
import numpy as np
from rdkit import Chem
import torch
import torch.nn as nn
from torch_geometric.nn import global_add_pool
from torch_geometric.utils import softmax, degree
from .mpn_att import MPN
#from torch.nn.utils.weight_norm import weight_norm
from chemprop.args import TrainArgs
... |
68e20dd16bd473b119c755d6346b22b7f830a792559892e8b099a7f49062ecd1 | Python | 9,463 | 248 | import os
import torch
import numpy as np
from tqdm import tqdm
from monai.transforms import LoadImaged, ScaleIntensityRangePercentilesd, Compose
from monai.data import ITKReader
from scipy.stats import entropy
from torch.nn.functional import softmax
from sklearn.metrics.pairwise import haversine_distances
from trimesh... |
336d1075642b92c8f2ff592683f04b711eeaea891f34dc369628fdce38fde8f7 | Python | 9,467 | 205 | """The HED character sets of specification section 2.2, loaded from the specification's own file.
``hed/validator/data/character_sets.json`` is a verbatim copy of ``character_sets.json`` as published by
hed-specification (``docs/source/_static/character_sets.json``). Both validators load the same file, so the
named se... |
ee21d485426200abb4212467e6985422e4205a1d2174e7beb315f56d032d5372 | Python | 9,467 | 264 |
"""
Created on Fri Jul 17 16:59:51 2020
@author: Leonardo Bonetti, Francesco Carlomagno
leonardo.bonetti@clin.au.dk
"""
#To use this script please do the following:
#-place the provided stimuli folders in your favorite directory
#-assign to the variable 'stimidr' (few lines below) such directory
#-define your log ... |
6898ad5b22e90a6cc34cd49f6bea5f2bb93bfb8f7a72faa74234c43745cce9d1 | Python | 9,468 | 291 | #
# Copyright Bradley Lowekamp
#
# 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.txt
#
# Unless required by applicable law or agreed ... |
77a85688e256c8378ada949994ad5d3b6fd128bdbd76bb254045014218dc8c87 | Python | 9,468 | 273 | # 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
# distributed under th... |
35bc333d5db614da83e40d6616039e19cbfdf5740e5c7da4c9a34fe4b6d18e29 | Python | 9,469 | 231 | r'''
This model fits the dipole and quadrupole of the inputs to the atomic charges
and predicts dipoles and quadrupoles. The dipole prediction uses a contribution from atomic dipoles.
The dipole moment is expressed as:
$$
\begin{aligned}
\mu = \sum_{i}{}^{3}\mathbb{P}_{i} + q_{i} \cdot \mathbf{r}_{i}
\end{aligned}
... |
3a3c78d0f22f7d8348d939d24a92640ba224c845534c393aeaf1e1f99773740d | Python | 9,470 | 286 | import os
from utils.embedding_utils import *
from classifiers.CustomClassifiers import AggregateClassifier
import numpy as np
from sklearn.base import BaseEstimator, ClassifierMixin
from sklearn.utils.validation import check_X_y, check_array, check_is_fitted
from sklearn.utils.multiclass import unique_labels
from skle... |
7fa5ddbfa9d338c5b8577fecc6ea5965eff2b3973cabff473f01ee6dbb3216a7 | Python | 9,471 | 184 | '''
Description:
Main codes for scNODE and Dummy model training and prediction.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import torch
from tqdm import tqdm
import numpy as np
import itertools
from model.layer import LinearNet, LinearVAENet
from model.diff_solver import ODE
from model.dynamic_model imp... |
a6193311bdba9811cd0e390dd1f214695f1bcb8f76d558e69662f53dbc2ddec6 | Python | 9,474 | 230 | """Batch orchestration for the tissue-masking tool.
Wraps :func:`process_group` in an iterable pipeline that supports
progress callbacks and cooperative cancellation, suitable for use
from a Qt worker thread.
"""
from __future__ import annotations
import os
import time
from dataclasses import dataclass, f... |
d7e0d813b96c148c9d16e5f777c0f3a71a9aa0f9a02420c071c45772ceba1380 | Python | 9,475 | 323 | # This code calculates the particle level gr for a binary system and then calculates the caging potential at a particle level. The local caging potential is coarse-grained to avoid fluctuations. local sop is reciprocal of the caging potential.
# Inputs : linked coordinates of big and small particles respectively. To ma... |
ee0d34194bed79a1035d6203c8af096109d68d151953f6530a81262720cefd68 | Python | 9,477 | 264 | from abc import abstractmethod
import numpy as np
from typing import Tuple
from typing import List
from shapely import geometry
from merlin.core import analysistask
class GlobalAlignment(analysistask.AnalysisTask):
"""
An abstract analysis task that determines the relative position of
different field of... |
b23602a280133ec6f9fa5fa73d987f3352549f7533ecfb28026d1dc49895a27c | Python | 9,478 | 193 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Created on Fri Apr 8 11:29:57 2022
# @author: caroline
"""
This script compute the weights given to reports of priors and implicit priors.
with a logistic regression (considering priors and sensory likelihood).
It select trials after the prior report.
Weights from th... |
0d7589c0ef8e896bf7ca8cee5f15bed591dd5692b47da12ad81279823a068f6a | Python | 9,481 | 210 | # -*- coding: utf-8 -*-
#
# Parameterization of neural power spectra with FOOOF - fitting oscillations & one over f.
#
#
#
# Builtin/3rd party package imports
import numpy as np
from fooof import FOOOF
import logging
import platform
# Constants
available_fooof_out_types = ["fooof", "fooof_aperiodic", "fooof_peaks"]
d... |
452c7ac7be471b3be75533b98e6eb9c197ab89be92b05ce07e44113c6f401d9f | Python | 9,481 | 210 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
5f72418f3760c8aaab05c543c1afb0c6b279ee27d081e37b3a620d061c158f2c | Python | 9,482 | 273 | """
Created in 2018
:author: Mahyar Osanlouy
:summary:
"""
import SimpleITK as sitk
import numpy as np
from skimage.exposure import match_histograms
__all__ = ['read_images_to_sitk_vector',
'read_image_to_sitk',
'calculate_origin_offset',
'sitk_resample_to_spacing',
... |
0c2a2cefb267e8aa22af4b80eb090e192e990cfdbb20d5bae9fe915f36b18548 | Python | 9,483 | 179 | import os
import re
from copy import copy
from typing import Dict, Tuple, Union
import numpy as np
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
class KFoldCrossSubject:
r'''
A tool class for k-fold cross-validations, to divide the train... |
5cfa1f28301090539734d459850e63afee2901974a03dcc5d97375412060d7b6 | Python | 9,484 | 228 | from typing import Tuple
import torch
from einops import rearrange, repeat
from einops.layers.torch import Rearrange
from torch import nn
def pair(t):
return t if isinstance(t, tuple) else (t, t)
class PreNorm(nn.Module):
def __init__(self, in_channels: int, fn: nn.Module):
super(PreNorm, self).__i... |
ce177bf1450f77bf7b324c36a3f5d3ddaa175f38dd213652ec485350dbdcab06 | Python | 9,484 | 272 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
a17712da37884c4e4571621de805eeb57f6da83f83b42c91f783bdbe47c89136 | Python | 9,486 | 263 | import contextlib
import logging
from abc import abstractmethod
from collections.abc import Generator
from contextlib import AbstractContextManager, contextmanager
from pathlib import Path
from time import sleep
from typing import Protocol
class _SynthesisFn(Protocol):
"""Synthesis function protocol.
A synth... |
14adae18ff2ee3a79de3b75cea452ff464f5d113398325332d3d316e2827712c | Python | 9,491 | 245 | """Implementation of input/output functions for .flag files."""
import warnings
import numpy as np
import scipy.sparse as sp
from ._utils import _extract_unweighted_graph, _extract_weighted_graph
def load_unweighted_flag(fname, fmt='csr', dtype=bool):
"""Load a ``.flag`` file and return the adjacency matrix of ... |
9434729dbae49fbe9766815521c6f40b532abb4bf3758e267590298c1be1a52b | Python | 9,491 | 300 | import numpy
from collections import namedtuple
from time import sleep
import sys
import time #@@@
import numpy as np
from scipy import misc
import cv2
try:
import gi
gi.require_version("Gst", "1.0")
gi.require_version("Tcam", "0.1")
from gi.repository import Tcam, Gst, GLib, GObject
except ImportError... |
7e0d8d8cfe6b880bd9be58b79776f608dd7b6c21d4291fd28b9be13460d6be55 | Python | 9,492 | 281 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.parameter import Parameter
import matplotlib.pyplot as plt
import operator
from functools import reduce
from functools import partial
from timeit import default_timer
from utilities3 import *
import os
import sys
sys.p... |
953a54341ab438f84430eff125964f954ce437a4870cadd04e2a2b00e878b678 | Python | 9,493 | 226 | """
Curates an output STAR file from Relion to work as input for pyseg.pyorg scripts for microtubules
Input: - STAR file with the particles to curate
- STAR file to pair tomograms used for reconstruction with the one segmented used to pick the particles
Output: - A curated output STAR file
... |
8e02fbafea1a58614afa273c0f9646a014da9e552b352bb22f202f4b713d474a | Python | 9,496 | 298 | import numpy as np
from scipy.sparse.linalg import cg, spsolve
from scipy.sparse import kron, diags, csr_matrix, eye, csc_matrix
from autograd import numpy as npa
from autograd import grad
from typing import List
solvers = [spsolve, cg]
def constraint_connectivity(
rho: List[float] = None,
nx: int = None,
... |
6d8fde2949d10bf66e46c24abcf8b80daf69aea2ec6098e7ca6a3099132f95a6 | Python | 9,498 | 231 | """
This script train a VQ-VAE style embedding network on Nanopore sequencing signal.
@author: Haotian Teng
"""
import os
import sys
import torch
import argparse
import numpy as np
from typing import Union,List
from itertools import chain
from torchvision import transforms
import torch.utils.data as data
from torch.ut... |
4784d5e10e62e7b86562d96119337a58f420bf7b31bf1bdc402f1f9b12287aa9 | Python | 9,499 | 242 | """
Elastix registration functions.
Runs elastix **in-process** via the ``itk-elastix`` library. The bundled
command-line ``elastix`` / ``transformix`` binaries were retired: every
operation the pipeline needs - registration, image transformation, and
point-set transformation - has a library equivalent here. T... |
2c2ad34035fb1cb49eaa5514f83bfafcb883677375a71a808f9df507eb781e30 | Python | 9,500 | 318 | import torch
import torch.nn as nn
def conv3x3(in_planes, out_planes, stride=1, groups=1, dilation=1):
"""3x3 convolution with padding"""
return nn.Conv2d(
in_planes,
out_planes,
kernel_size=3,
stride=stride,
padding=dilation,
groups=groups,
bias=False,
... |
81a39d12a705af9c210a522ae83e48b09ecfeeaffbe09e41a10960c65c96b396 | Python | 9,503 | 287 | import copy
import logging
import numpy as np
import scipy.signal
from importlib import import_module
from sleeplab_format.extractor.config import ArrayAction, ArrayConfig, SeriesConfig
from sleeplab_format.models import ArrayAttributes, SampleArray, Series, AASMSleepStage, Subject
from typing import Callable
logger... |
326dbe2065e870bcffca3ae3599f862446e200c63642a524f8a448b1603b8a41 | Python | 9,505 | 314 | import re
from abc import abstractmethod
from collections.abc import Callable
from itertools import chain
from typing import Concatenate, Iterable, Protocol, cast
import elasticai.creator.ir as ir
from elasticai.creator.graph import find_all_subgraphs
from elasticai.creator.ir import (
AttributeMapping,
Edge,
... |
2293f5e3dfb0be301e114e1be9da86fc2c4ee5e21469fcf53d45e1c04e7143eb | Python | 9,506 | 203 | # coding=utf-8
# Copyright 2020 Google and The HuggingFace Inc. team.
#
# 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... |
031b44433e173b5585ed91f7f91c131620eba6c6bea3f5f4e8877e46d5a7bb93 | Python | 9,507 | 225 | # coding=utf-8
# Copyright 2020 The Facebook AI Research Team Authors and The HuggingFace Inc. team.
#
# 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/LIC... |
2a724f88e69b935e392cc9e13dd2735ee67d1f7706d3011ce9e394ef9f679382 | Python | 9,510 | 208 |
# imports
import numpy as np
import pandas as pd
from sklearn.linear_model import Lasso, Ridge, ElasticNet, RidgeCV
from sklearn.kernel_ridge import KernelRidge
from sklearn.pipeline import make_pipeline
from sklearn.svm import SVR, LinearSVR
from sklearn.compose import ColumnTransformer
from sklearn.compose import ... |
1d69f4f4f41e4585e5ba31bdccda326f69a26d5dedb15e2bf99fc38f8a2942bc | Python | 9,511 | 272 | # encoding: utf-8
import _init_paths
import fire
import time
import pandas as pd
import os
import numpy as np
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision
import torch.nn.functional as F
from tqdm import tqdm
from collections import OrderedDict
from torchvision import da... |
5a965634594881fa7c6a5fb5cd68c17b8e5a9ed4edaf885d95c906605c404eb6 | Python | 9,511 | 235 | '''MIT License
Copyright (c) 2020 Duncan Forster
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, p... |
bf5e555959a975a1b8030d5b06f6578416ce819fb3abba8cda1965f16a9a5d6a | Python | 9,511 | 262 | import nibabel as nib
from nibabel import processing
import matplotlib.pyplot as plt
import numpy as np
import os
import argparse
import pandas as pd
from sklearn.preprocessing import QuantileTransformer
import logging
from tqdm import tqdm
def create_logger(log):
"""
Creates a logger that logs to both a file ... |
dab3784b63c4f19153af41314d95c4532e3608b6d6d4948a5b8b16cf07c5aa26 | Python | 9,512 | 253 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Defines classes and methods used by example_parallel_network.py script
Copyright (C) 2018 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
t... |
8b31ca5ec8db594ef397753e79742614aeba082a6e948dcccf0c64c770acf79e | Python | 9,513 | 276 | import os
import copy
import yaml
import argparse
import ray
import utils as u
logger = u.getLogger(__name__)
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument(
'-c',
'--experiment_config',
required=True,
type=str,
help='Format: exper... |
a0bd5b04ff99ec9310823800ebd4903efd734bdce3bf1827e92e0d4232b89fb1 | Python | 9,513 | 231 | # -*- coding: utf-8 -*-
"""
Created on Mon May 23 22:07:30 2022
@author: ftead
"""
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy import stats
import math
import re
from matplotlib_venn import venn2
import gseapy as gp
#%%
#Took the data th... |
d30e72ce006f3ac5e7ac4250c775f07b02711ead1238794eaa555102f6100ec7 | Python | 9,513 | 260 | import sys
import random
import os
import argparse
import sys
import pwd
import time
import subprocess
import re
import shutil
from sklearn import metrics
import re
from sklearn.metrics import roc_curve,roc_auc_score
import numpy as np
import glob
from sklearn.metrics import roc_curve,roc_auc_score
from sklearn.metrics... |
22cb23946553897c596cc454dd76b95aaa9089c798852c9733264e909ea93e4d | Python | 9,515 | 249 | from itertools import chain
from typing import List, Tuple
import numpy as np
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
from torch.autograd import Function
from torch.utils.data import DataLoader
from ..classifier import ClassifierTrainer, classification_metrics
class Dua... |
2f0f043648a121e08e97d4551b9dc44df2864684917cddb82db9b7f2fa2e9f70 | Python | 9,516 | 269 | # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/03_models.ipynb.
# %% auto 0
__all__ = ['ToyODE', 'make_model', 'Autoencoder', 'ToyModel', 'ToySDEModel']
# %% ../nbs/03_models.ipynb 3
import itertools
from torch.nn import functional as F
import torch.nn as nn
import torch
class ToyODE(nn.Module):
"""
OD... |
41e7ba2bc3978c6b1ebc2d714cdf251505b62796079e395fa9353302eef6bee3 | Python | 9,518 | 261 | import math
import torch
from torch import nn
class PositionalEmbedding(nn.Module):
"""Positional embedding layer for sequence data.
Args:
d_model (int): The dimension of the model.
max_len (int): Maximum sequence length. (default: :obj:`5000`)
"""
def __init__(self, d_model: int, ma... |
d9621d2044b8a07413c9ff16eff253373a7e9373899dc5080c0b480be4e42feb | Python | 9,518 | 157 | r"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into bu... |
0bef2956d57662db3837d6736895f13794d203eff5a0448eecd84ee7e6a28e59 | Python | 9,521 | 250 | # -*- coding: utf-8 -*-
#
# Logging functions for Syncopy.
#
# Note: The logging setup is done in the top-level `__init.py__` file.
import os
import sys
import logging
import socket
import syncopy
import warnings
import datetime
import platform
loggername = (
"syncopy" # Since this is a library, we should not u... |
3811420cd4403bb50fb7235ef2bbad9b343676087eb9b5799edbde51da16f0a2 | Python | 9,521 | 277 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
2f4a019d640ef833bbf96e51a9aba31331842406bb8270181e0786167744e801 | Python | 9,522 | 246 | import os
import glob
import pandas as pd
import re
import matplotlib.pyplot as plt
import numpy as np
from sklearn.metrics import mean_squared_error, mean_absolute_error, r2_score
import mne
from mpl_toolkits.axes_grid1 import make_axes_locatable
directory = "Results_files/KMER_gamma_free_0.1-1-10/"
# Get all files m... |
e3137adc38dfb03d6c72d25ce2b9667f105def6964d7dbc1660c2a062cab7f74 | Python | 9,523 | 276 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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... |
e8973a5b5783641cf216ed49d18adc74d155042f9120dba3666bde4a707c471c | Python | 9,523 | 299 | # exceptions.py
import re
import sys
import typing
from .util import (
col,
line,
lineno,
_collapse_string_to_ranges,
replaced_by_pep8,
)
from .unicode import pyparsing_unicode as ppu
class ExceptionWordUnicode(ppu.Latin1, ppu.LatinA, ppu.LatinB, ppu.Greek, ppu.Cyrillic):
pass
_extract_alp... |
060db14a23e3d8ede2375034528def441728d610cb6ac2a51cd1c292a96f1f8f | Python | 9,524 | 208 | # -*- coding: utf-8 -*-
from __future__ import annotations
from typing import List, Optional
import torch
from supar.structs.dist import StructuredDistribution
from supar.structs.semiring import LogSemiring, Semiring
from torch.distributions.utils import lazy_property
class LinearChainCRF(StructuredDistribution):
... |
a547953d13d7e2fa38cf9c31c12a6eb91ec3e809ae35b596c89f7133cf9addde | Python | 9,524 | 278 | import sys
from collections import defaultdict as d
import re
from optparse import OptionParser, OptionGroup
#Author: Martin Kapun
#Modified by: Siyuan Feng
######################################################### HELP #########################################################################
usage="""python %pro... |
6b810c9b319412e395d41ddeb78247f653ec1fe3adc10602340acc9d4c6d23d8 | Python | 9,529 | 191 | import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import matplotlib.animation as animation
import time
import ray
import os
from neuron_model_parallel import NeuronSim
from elec_field import sparse_place_human
from pulse_train import PulseTrain_Sinusoid... |
d2de5cc42829ebb11bb66ca6f1984f9689fa8035869111054d72c762f07530f9 | Python | 9,531 | 269 | """
Script for applying RWR to GraphMCF
Input: - GraphMCF instance (pkl)
Output: - GraphMCF with the result of RWR added as a new prop
"""
__author__ = 'Antonio Martinez-Sanchez'
# ################ Package import
import sys
import time
import getopt
from graph import GraphGT
from globals import *
f... |
dcfb910c3b6956949103e6344e6666f0b4a07d0c2495a4eae63b3a3ac814cedb | Python | 9,531 | 225 | """ Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This is the main file provides MULTICLASS (CNN and ViT) models for end-to-end solution for what is mentioned in the paper.
# Update paths to processed datasets
if __name__ == '__main__':
import warnings
warnings.simplefilter(action='ignore', ca... |
a0b7a5f3620b097b03432f5ea065f0c8cdab0c7796825cf1e6b6b0f19c703ae9 | Python | 9,533 | 270 | #
# Result post-processing utilities for ACME
#
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
# Builtin/3rd party package imports
import os
import sys
import shutil
import logging
import h5py
import numpy as np
from typing import Union, List, ... |
566389055e630eb22993acf774dd7276e2b2548e1256ea1d495dfbb93e2d2df9 | Python | 9,535 | 285 | from collections.abc import Callable
from functools import singledispatchmethod
from re import Match, Pattern
from re import compile as _regex_compile
from typing import Iterable, Protocol, runtime_checkable
@runtime_checkable
class TemplateParameter(Protocol):
regex: str
"""A regular expression to match what... |
6a1caa1f312dfe8d143178c72da5ed7831a7bdf8f6814b4fcc2fc6bbb1673eda | Python | 9,535 | 260 | # -*- coding: utf-8 -*-
from __future__ import annotations
from typing import Callable, Optional
import torch
import torch.nn as nn
from supar.modules.mlp import MLP
class Biaffine(nn.Module):
r"""
Biaffine layer for first-order scoring :cite:`dozat-etal-2017-biaffine`.
This function has a tensor of w... |
ae0aed432cf309586cd4986f4f74911f6682f3f29fa4817a4954c23bf2275dd3 | Python | 9,536 | 163 | import time
import numpy as np
class ParameterSimulator:
def __init__(self, adapter, simulator, verbose):
if verbose:
print('Initialising Evaluator')
self.adapter = adapter
self.simulator = simulator
self.verbose = verbose
'''functionality'''
def simulate_thet... |
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