sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bb8b861b9ae2baccae8d30ad538f949f60e4b86880be75e2db6fcfaa2352455a | Python | 7,945 | 196 | # File to generate a blender FBX from the SEEG data
# Load libraries
import argparse
import os
import bpy
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import scipy.signal as signal
from sklearn.preprocessing import normalize
from segmentation import export_probes_as_obj, segment_electrodes, el... |
d7bc370d622a2b881e3c14cd62288c0a2bc0c465007ece124953eb4a1e453a19 | Python | 7,948 | 247 | #
# 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,... |
d090531a04e7cc9e4093b80a2de12a321d3b019d559e2dab950e53e0ea0536b4 | Python | 7,949 | 178 | # -*- coding: utf-8 -*-
from __future__ import print_function
import os
from .util import DRIVER_DIR
PORTFOLIO_DIR = os.path.join(DRIVER_DIR, "portfolios")
ALIASES = {}
ALIASES["seq-sat-fd-autotune-1"] = [
"--evaluator", "hff=ff(transform=adapt_costs(one))",
"--evaluator", "hcea=cea()",
"--evaluator"... |
55848985831630649bc8a656ef3512e4fc0a28931fb25c3802c0147a8885725d | Python | 7,950 | 192 | import cc3d
import numpy as np
import cv2 as cv
import matplotlib.pyplot as plt
import SimpleITK as sitk
from tiffile import imread, imwrite
from skimage.measure import label, regionprops
from skimage.transform import warp
from scipy.interpolate import RBFInterpolator
from scipy.spatial.distance import cdist
class Po... |
99131aaf89cf1a520d2c2af77713a0aafe90ade121c19c36e0cb7da9f18e6e88 | Python | 7,950 | 249 | # 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... |
33e1900727516473978a78c1d99731869ff40a35f6bc937149763086732550e9 | Python | 7,952 | 187 | import math
import os
import shutil
from multiprocessing import Manager
from typing import Any, Callable, Union
from joblib import Parallel, delayed
from tqdm import tqdm
from torcheeg.io import EEGSignalIO, MetaInfoIO
def _set_files(**kwargs):
root_path = kwargs.pop('root_path', '.') # str
num_samples_per... |
be1968a4fef12c765ef2e8ffa9e17c40018cc41fab0351b00c0fc1fd416c077a | Python | 7,954 | 143 | # 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... |
138501e93cc73446540854d4f4f3f2d5a745add8930559362c38ac42dc3d4e03 | Python | 7,958 | 109 | """FLYVIS_CENSUS.py 2026-10-05. Pre-registered: 04-NOTES/PREREG-2026-10-05d-FLYVIS-CENSUS.md (sha in .sha256 next to it).
Sign census in Lappalainen et al.'s connectome-constrained visual system models (flyvis 1.2.0, ensemble flow/0000):
reverse each source cell type's signs, measure T4/T5 direction selectivity on movi... |
29175879e709c02bab6a465a7caf64070d963fb98f781d4ce6ec2bc0030da6c0 | Python | 7,960 | 250 | """Schemas for storing thermo data."""
from __future__ import annotations
from logging import getLogger
from typing import TYPE_CHECKING, cast
from ase.thermochemistry import HarmonicThermo, IdealGasThermo
from ase.units import invcm
from emmet.core.symmetry import PointGroupData
from pymatgen.io.ase import AseAtoms... |
e03ad909e0155b099e8ac234da1956ecdf4b296ca8fea5e56c12f847452899ac | Python | 7,962 | 226 | import numpy as np
import pyqtgraph as pg
import pyclamp.gui.pyqtplot as pq
from pyclamp.dsp.lsfunc import *
from pyclamp.dsp.fpfunc import *
from pyclamp.dsp.fpanal import *
from pyclamp.gui.xyfunc import *
from pyclamp.gui.pyplot import *
from pyclamp.gui.pydisc import *
class pywavescattabl (pywavescat) : # combine... |
e6c027971b09d4ec01a5029ccee0c9b440603eae62e1bac158511025bcd8a2ea | Python | 7,962 | 255 | """"""
"""
Prosper_nn provides implementations for specialized time series forecasting
neural networks and related utility functions.
Copyright (C) 2022 Nico Beck, Julia Schemm, Henning Frechen, Jacob Fidorra,
Denni Schmidt, Sai Kiran Srivatsav Gollapalli
This file is part of Propser_nn.
Propser_nn is free softw... |
43b2d0100df4d6be0fb3b0e7b3267850d40594f33ca7b987a9f668a2456977d6 | Python | 7,964 | 190 | import torch.nn as nn
import torch.nn.functional as F
import torch
class ATCNet(nn.Module):
r'''
ATCNet: An attention-based temporal convolutional network for EEG-based motor imagery classification. For more details, please refer to the following information:
- Paper: H. Altaheri, G. Muhammad and M. Alsu... |
4641b612f2ca784520655f8fdfad98f901f9edd3263aa7b4efc998556f119386 | Python | 7,965 | 183 | #
# 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,... |
6db8bd998db8aee926fd8fb901ce7dba657e546fcd6f475a0b206d4577d0bbbe | Python | 7,965 | 215 | from __future__ import annotations
import logging
from pathlib import Path
import numpy as np
import pytest
from ase.build import molecule
from ase.calculators.emt import EMT
from ase.units import invcm
from monty.json import MontyDecoder, jsanitize
from monty.serialization import loadfn
from quacc.schemas.thermo im... |
a35c895d0ce0183a813dd26ac673d3ec83b741cc713d616c5cbcdab1d9730d43 | Python | 7,965 | 217 | # Import required libraries
import numpy as np
import random
# Define global variables
MIN_WAVENUMBER = 0.1
MAX_WAVENUMBER = 2000
def key_parameters(a=5, b='b'):
"""
Define key parameters based on input case.
Returns:
tuple: (min_features, max_features, min_width, max_width)
"""
# Define ... |
bfeeba93def42f2db5221dc40bf7d0cce6efd912ef9c7908b9a0c3ab1e0c059a | Python | 7,965 | 221 | import csv
import gc
import gzip
import os
import pickle
from datetime import datetime, UTC
from codex.data.neuron_data_initializer import (
initialize_neuron_data,
NEURON_DATA_ATTRIBUTE_TYPES,
)
from codex.data.versions import DEFAULT_DATA_SNAPSHOT_VERSION, DATA_SNAPSHOT_VERSIONS
from codex.utils.networking i... |
2fe1b57378c2407171c56e88389e9b7055c9ce0167110a8371e66fe7f4dbe0ed | Python | 7,967 | 255 | # 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... |
7f13a7262c9b8ade2655d53f2fb4e7191f30ff99a14207f880271d38af696640 | Python | 7,968 | 174 | import argparse
from loader import BioDataset
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from tqdm import tqdm
import numpy as np
from model import GNN
from sklearn.metrics import roc_auc_score
import pandas as pd
from util import ExtractSubstructureContextPair
... |
74c885412bd898056f58dee0f36197e5a7c6ee64abf22fe22bacf661b12acb7a | Python | 7,970 | 215 | import multiprocessing as mp
import os
from functools import partial
import numpy as np
import tqdm
from skimage import measure
try:
import ray
except ImportWarning:
pass
from plantsegtools.utils import filter_2d_masks, smart_load, relabel_segmentation
def mask2mesh(mask, mesh_processing=None, voxel_size=(... |
595f8ea3786c92f4b847f235aee884049b1d61308aa0b1750ba21faa575374f5 | Python | 7,971 | 210 | """Qualitative comparison of static M/EEG resting-state networks
"""
# Set up dependencies
import os
import numpy as np
from sys import argv
from osl_dynamics.analysis import static, power, connectivity
from osl_dynamics.data import Data
from utils.data import load_data, save_data, get_raw_file_names
from utils.stati... |
06b4dfb8ffe2a6c750541d517eea369c307a73ea095d61bd809900e9edf181c3 | Python | 7,973 | 231 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import global_mean_pool
from torch.nn.modules.batchnorm import _BatchNorm
import torch_geometric.nn as gnn
from torch import Tensor
from collections import OrderedDict
'''
MGraphDTA: Deep Multiscale Graph Neural Network for Exp... |
4069038bb1cddd1ca896f4575e52b1d9a7d5360a82918d05153ae8776d61f63c | Python | 7,973 | 231 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import global_mean_pool
from torch.nn.modules.batchnorm import _BatchNorm
import torch_geometric.nn as gnn
from torch import Tensor
from collections import OrderedDict
'''
MGraphDTA: Deep Multiscale Graph Neural Network for Exp... |
683bbd043a047226a96274c23e8f8d823fd1aee3b81f227c15acb2b7dbbef5ed | Python | 7,973 | 231 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import global_mean_pool
from torch.nn.modules.batchnorm import _BatchNorm
import torch_geometric.nn as gnn
from torch import Tensor
from collections import OrderedDict
'''
MGraphDTA: Deep Multiscale Graph Neural Network for Exp... |
d890db22c6cb7ed8f837f4f9f842af6b4f23793132703a157f4a7b89b171c074 | Python | 7,973 | 231 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import global_mean_pool
from torch.nn.modules.batchnorm import _BatchNorm
import torch_geometric.nn as gnn
from torch import Tensor
from collections import OrderedDict
'''
MGraphDTA: Deep Multiscale Graph Neural Network for Exp... |
5fc63cc2bf6092b9525792e1e9e578a3ecc0be35ac1709f7a6168d448c3079ff | Python | 7,974 | 230 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import os
from collections import defaultdict
from fvcore.common.file_io import PathManager
from datasets.ava_eval_helper import read_exclusions
logger = logging.getLogger(__name__)
FPS = 30
AVA_VALID_FRAMES ... |
f2d7937753fd3c92aecd34ebf56913b957f862caf167f990eac3a71c413e7aa4 | Python | 7,974 | 215 |
from scipy import io, sparse
import os
import pandas as pd
import numpy as np
class SingleData(object):
"""
A single modality of a single dataset
Parameters
----------
feature_name
Name of the modality
dataset_name
Name of the dataset
feature
Array of length F co... |
0dd83b424a1cc10f26acee82591ff899a76dd9ce40dac7275fcb23d4ce65e845 | Python | 7,977 | 197 | #
# 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,... |
94f558896b12b84817b77b399ad7cead4fc98b8d171007a5a80860ab4d7e0b41 | Python | 7,977 | 308 | # 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... |
9b553a1c28d970c30667c82de45ad9c0ee779e616e01a889fd75e5501e0820b2 | Python | 7,977 | 219 | import logging
from pathlib import Path
import numpy as np
import numpy.testing as npt
import pandas as pd
import pytest
from vascpy import PointVasculature
import astrovascpy.utils as test_module
from astrovascpy.exceptions import BloodFlowError
L = logging.getLogger(__name__)
TEST_DIR = Path(__file__).resolve().p... |
4559d20c66456f2fbac30aca212fd1305b4246f26240cb1573ddd5612bebc31d | Python | 7,979 | 222 | # 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... |
82ee1ac5d505eeba1588a30ded3e71699f9d4b3c84f2e5282f34075bcc2e509f | Python | 7,980 | 217 | from functools import partial
import numpy as npo # original numpy
from numpy.lib.stride_tricks import as_strided
import autograd.numpy as np
from autograd.extend import defvjp, primitive
@primitive
def convolve(A, B, axes=None, dot_axes=None, mode="full"):
if dot_axes is None:
dot_axes = [(), ()]
... |
b62c77b1f93dd99194ed3faaed0873d4bc50ece4c675532ca9f2ff4bb1083cbd | Python | 7,980 | 201 | import torch
import json
from datasets.utils import *
class SrcLang:
def __init__(self, vocab_path):
self.word2index = {}
self.word2count = {}
self.index2word = []
self.n_words = 0
self.get_vocab(vocab_path)
self.class_tag = ['[PAD]', '[GEN]', '[POINT]', '[NUM]', '[... |
25afb8045a779f0e23d89bcdaab7bab2c6942ffef7ad6ea7dccad1767ccde10f | Python | 7,981 | 164 | ############################################
######## Inference Prod Conditional ########
############################################
#%%# Catalyzer
# import re
import numpy as np
# import numba
# from scipy import interpolate
import torch
from sbi.inference import SNPE
from sbi import analysis
import time
import m... |
1b98a54716c76fb2b2d26c374cec53180107364b3cc0d49734725d4c7379ff02 | Python | 7,982 | 188 | import unittest
import os
import pandas as pd
import sys
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../../src")
from hornet.model import train
class TestTrainFunction(unittest.TestCase):
def setUp(self):
self.path = ".output_test_train"
self.input_path = ".input_test_train"
... |
31d1de1bf36fb34bb4fcd77ea3ea73e4b63cf7aa42adf73158b5c9da86ea0956 | Python | 7,983 | 266 | import sys
import time, datetime
from os.path import join, dirname
import json
from collections import namedtuple
from math import ceil
from tqdm import tqdm
from tqdm.utils import disp_len, _unicode
import numpy as np
from .mpi import is_master
class mytqdm(tqdm):
def __init__(self, iterable=None, **kwargs):
... |
7e262d28388a88d53fa15368df6fb9840517a8dc5f8f6dd07684063a54b7d40f | Python | 7,985 | 213 | import os
import torch
import time
from core.utils import *
from datasets.meters import AVAMeter
def train_ava(cfg, epoch, model, train_loader, loss_module, optimizer):
t0 = time.time()
loss_module.reset_meters()
l_loader = len(train_loader)
model.train()
for batch_idx, batch in enumerate(train_... |
f86f24ba440ee054aeebf6733cf8e41cb699cf0058d3346cecb9222bd662c80b | Python | 7,985 | 260 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
76773dd3e90927c4a5cbc76cb6c6a4e11c1e8f2e95e4a9a162659c529923abba | Python | 7,988 | 172 | """Driving the two-point midline from actual mouse clicks.
``begin_midline_drawing`` / ``_on_midline_click`` and the ``from_two_points``
geometry already exist and are pinned by ``test_midline_two_point_draw.py``.
What was missing is everything between a user's mouse and that arithmetic:
nothing in the panel was ... |
aa32c6d43ecb82c372cd3bff79e8706c563b8bdc468059350e77ad9ace735300 | Python | 7,992 | 205 | """
Transfer Learning from MAHNOB-HCI to DEAP
=========================================
In this tutorial, we demonstrate how to use TorchEEG to implement transfer learning with a Continuous Convolutional Neural Network (CCNN) model. We'll train our model on the MAHNOB-HCI dataset and then apply it to the DEAP dataset.... |
b875295b598a6c8d071191f2d4a64499271493b6702897c1d9f6901d81cae164 | Python | 7,993 | 208 | import bct
import networkx as nx
import numpy as np
from tqdm import tqdm
from sklearn.utils import check_random_state
def strength_preserving_rand_sa_dir(A, rewiring_iter = 10,
nstage = 100, niter = 10000,
temp = 1000, frac = 0.5,
... |
0b9da28720e59a08099005deb3975c69aab4642e780d9ab5ba3df3d74c30e714 | Python | 7,994 | 253 | import numpy as np
from numpy.typing import NDArray
from scipy import signal
def aud_space_bw(
fmin: float,
fmax: float,
bw: float = 1.0,
scale: str = "erb",
) -> NDArray:
"""Auditory scale points specified by bandwidth. It computes a vector containing values equidistantly scaled between
frequ... |
18c9a29373c96aa5733588a707a2fc0885ae462eba05db0c60d175cfd7c4adb1 | Python | 7,995 | 308 | import math
import numpy as np
import scipy.signal
import scipy
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from scipy.signal import blackmanharris, correlate
import scipy.ndimage
from sklearn.cluster import AgglomerativeClustering
from sklearn.metrics import silhouette_samples, silhouette_score
def fin... |
2708a0f21ff58ce63167aa5958c5d429ba1774befd7a1467d00e909aa2f934e2 | Python | 7,999 | 197 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Nov 2 12:26:37 2023
@author: Dustin Garner
"""
import math
import datetime
import numpy as np
import pandas as pd
from fafbseg import flywire
import flycode.mapping as mapping
import flycode.utils as utils
import flycode.flywire_functions as fw
clien... |
e58ed1e7ee71e6d1bb75e61d89db5a41f25a86064fdbff4dd9d658197afcc203 | Python | 8,000 | 261 | """Parallelization and time recording
-------------------------------------
"""
import time
import numpy as np
from mpi4py import MPI
# initialize MPI
COMM = MPI.COMM_WORLD
SIZE = COMM.Get_size()
RANK = COMM.Get_rank()
def run_parallel_functions_sequentially(funcs, filename):
'''
Runs parallelized functions... |
ee60f508dd2ef0a2bb8747989c983a3aa52cc47fd3a87adbd80c531efb3a87e5 | Python | 8,000 | 180 | from wsilearn.utils.cool_utils import *
from wsilearn.utils.path_utils import *
def make_link(src, link, relative=False, ssh_node=None, verbose=False, dry_run=False, exist_ok=False):
if exist_ok and Path(link).exists():
return
if relative:
src = os.path.relpath(str(src), Path(link).parent)
... |
78ec30c2b79942b86aaf2bd1d86e1608dcea473f57c3ff047a905476953168ff | Python | 8,004 | 250 | #
# 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,... |
e1ae4129ba126d4a43a5ab4f5a1f76ebcd3b6f3beb347fe9c170501a76e2b6cd | Python | 8,006 | 145 | from Bio import SeqIO, motifs
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
import matplotlib.pyplot as plt
import matplotlib
from scipy.ndimage import gaussian_filter
from torchmetrics.image.fid import FrechetInceptionDistance
import torch
import lightning.pytorch as pl
from hicdiffusion_m... |
8ba044c9fba3b5a2a7858f0fd9e3f32f4731a533bab62db4496af98cc44463f1 | Python | 8,007 | 182 | from typing import List, Tuple, Union
import numpy as np
import torch
from torch import Tensor, nn
from torch.nn import functional as F
from torch.utils.data import DataLoader
from ..classifier import ClassifierTrainer
class FocalLoss(nn.Module):
def __init__(self,
gamma: float = 1.0,
... |
e3c76d56def26867a30d30a872f82744deace8549dd19ceec0f73aff5d8e85dc | Python | 8,007 | 258 | #!/usr/bin/env python3
from pathlib import Path
import csv
import shutil
import numpy as np
import nibabel as nib
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from nilearn import datasets, plotting
from nilearn.image import load_img, resample_to_img
# -------------------------------------... |
49b758491de8d32efaf7d23fe734e93107a1cb77d491644b260529dc5ba650bc | Python | 8,009 | 240 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.linear import Linear
from elasticai.creator.nn.integer.mha.design import MHA as MHADesign
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQP... |
d11fc94bc1a5542ec724504c9ce0086a094e867905b3ac2df284cfdf43046ffa | Python | 8,009 | 211 | from __future__ import annotations
import json
from collections import ChainMap
from pathlib import Path
from typing import TYPE_CHECKING, Literal
import pandas as pd
from scanpy import settings
from pertpy.data._dataloader import _download
from ._look_up import LookUp
from ._metadata import MetaData
if TYPE_CHECK... |
040724cf87e9e06676c58af10cb7c27c8f86af8e29823f30e71dc2cce054a652 | Python | 8,013 | 258 | # 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... |
f834a5e087db38e0014dd6f9dd28add3e52b7c39e2e5e0e17a73b5f8b9954083 | Python | 8,013 | 155 | """Launch the local anatomical neural observatory or run a real diagnostic."""
from __future__ import annotations
import argparse
import json
import logging
import os
from dataclasses import fields
from pathlib import Path
ROOT = Path(__file__).resolve().parents[2]
def load_configuration(path: Path, cpu: bool = Fal... |
1effb6c5b54b5bc73e81a199775ff2638714c185141a36a25c219b195b2eaec4 | Python | 8,014 | 234 | # 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... |
24a0799094ea9477e8d08862037d745cbd026c097c7d9c2fd914137da0493e15 | Python | 8,014 | 238 | """
Class for corresponding points, i.e. correspondences.
"""
from pathlib import Path
import numpy as np
import pandas as pd
from scipy import spatial, stats
from . import pointcloud
class CorrPts:
"""Class for managing corresponding points between two overlapping point clouds."""
def __init__(self, pc1:... |
e3e2c7b865c30e7bf3ff5670a34ad97c05f4e8f8524f23a5cb27c9c82bead565 | Python | 8,016 | 241 |
## Multi-animal
# you might have to set cuda_visible in terminal before launching python
import os
os.environ['CUDA_VISIBLE_DEVICES'] = '0'
device = 0
import multiprocessing
import numpy as np
# multiprocessing.set_start_method('spawn')
import nvidia_smi # Install using pip install nvidia-ml-py3
import time
lbl_fi... |
58b93e324ff71b6092bd7ddd5cd6335d683315849f49f3febce62c11b31d78d8 | Python | 8,018 | 221 | # Motionmapper-esque. Uses UMAP for dimensionality reduction rather than tsne
import sys
import os
import glob
import yaml
import numpy as np
from matplotlib import pyplot as plt
from tqdm import tqdm
import scipy.signal as signal
from scipy import ndimage as ndi
import scipy
import sklearn
import umap
from BEBE.models... |
c76ca9654ffd15a8b8af57f3d6712aa09ade39152def0b0a9ce28efd285aad27 | Python | 8,018 | 239 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : benchmark.py
# Author : Yufeng Liu
# Date : 2023-04-04
# Description :
#
#=====================... |
1cea403fe8e96a4e96ac77fe1a286a16f4c3e437ce194ceb7b8e29d31511570d | Python | 8,020 | 241 | """
In a Relion's STAR file sets prior columns values as a copy of the rotation angles.
VERY IMPORTANT NOTES: Relion reconstructs move particles to reference, in contrast refinement procedures,
so euler angles must ve swapped and inverted for generating the prior information.
... |
75603e0d3bd97d00a94d122d14c90ed774c35fa9eac8cfa0a36a0734bf7214e5 | Python | 8,020 | 199 | """
Run custom setup when MolecularNodes node group assets are added to a tree.
Since the node groups are shipped as regular assets in an asset library, no
MolecularNodes code runs when a user drags one into a node tree. The
``blend_import_post`` handler fires for every link/append operation — including
asset drag-and... |
b729269d5f9a6611c6eea31eb0cc8e67e6d53126cd385ded3ad3ed4674478acf | Python | 8,021 | 185 | """Functions to evaluate the performance of the translation model during training"""
import multiprocessing as mp
import csv
import os
import numpy as np
import pandas as pd
import tensorflow as tf
from sklearn.svm import SVC, SVR
from sklearn.model_selection import LeaveOneGroupOut
from sklearn.preprocessing ... |
e82d25d3ff7785e707f9f3382ceef2a28361659522be9ca723a9d595c20dcb30 | Python | 8,023 | 282 | # Abstract database class supporting datasets, categories, views, feature sets, users, jobs, and job results
# Only methods server and datasets must be supported in 'client' mode
import os
from cirrocumulus.envir import (
SERVER_CAPABILITY_ADD_DATASET,
SERVER_CAPABILITY_DELETE_DATASET,
SERVER_CAPABILITY_ED... |
dc57012680838329b5dbf74deb17caf02d6044e6341e7e0d488daef31bf9d2e1 | Python | 8,024 | 228 | # Copyright 2016–2021 Julien Danjou
# Copyright 2016 Joshua Harlow
# Copyright 2013-2014 Ray Holder
#
# 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-... |
cfba1f865349a618b4e54f9e581bc0d870370dbefa2a3dbbf06bfcbc0052988c | Python | 8,028 | 168 | # coding=utf-8
# Copyright 2021, The Facebook AI Research Team and The HuggingFace Inc. team. 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.or... |
2716230f467f7e605d65dc19c3d948a4265e7df88cb4aa664d6fea7b7240282e | Python | 8,029 | 225 | #!/usr/bin/env python
'''
LFP simulation script for 4x4 mm2 network model
But the network is implemented with spatial connectivity, i.e., the neurons
are assigned positions and distance-dependent connectivity in terms of
cell-cell connectivity and transmission delays.
Synopsis of the main simulation procedure:
1. Loa... |
3888a9f91e49f76256894dc5c3401a3640c18dde2c7df50e2298814dd94fa333 | Python | 8,033 | 188 | # Librairies
import os
import sys
code_path = os.path.split(os.path.split(os.getcwd())[0])[0]
sys.path.append(code_path)
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import argparse
import json
import seaborn as sns
from matplotlib.colors import ListedColormap
from setting import *
from u... |
010be9015b4feef4d309482d79c8ffe2d57fa7ab103023e0b7bbbe8ad7b2ae23 | Python | 8,034 | 188 | import numpy as np
import cv2
from typing import Tuple
from merlin.core import analysistask
ExtentTuple = Tuple[float, float, float, float]
class GenerateMosaic(analysistask.AnalysisTask):
"""
An analysis task that generates mosaic images by compiling different
field of views.
"""
def __init_... |
5e899782b0ed008d9ece4f575f9b56466e63c892b10998b50506bf30eb5fd15d | Python | 8,035 | 210 | import torch.nn as nn
import torch
import torch.nn.utils.prune as prune
from typing import Optional, Type
from operator import xor
class HCNNCell_compressed(nn.Module):
"""
The HCNNCell call is implemented to model one forecast step in a Historical Consistent Neural Network
with compressed support input.
... |
faeb4d792646bc89a54f7dafd4a7ae6d55eba422df30bc9ce35470b6627219a2 | Python | 8,035 | 196 | #!/bin/env python
"""
OXASL - Distortion correction module
The functions in this module calculate non-linear distortion correction transformations
to apply to the ASL and calibration images.
Currently two sources of transformation exist:
- Fieldmap-based distortion correction. This generates a nonlinear warp image
... |
d3ba7d4136b9a6b2d96648d2c077fa5b21f14701976080f3d56dbe12e0020fb5 | Python | 8,039 | 168 | # coding=utf-8
# Copyright 2021, Google and The HuggingFace Inc. team. 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
... |
c55a6d961821817698e6baef6cde2dcbfa5f0799f7ad8397ab4dd6f842c8f0f6 | Python | 8,040 | 170 | """A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
import pathlib
here = pathlib.Path(__file__).parent.resolve()
print("her... |
2bb5cb83f1268aa39badc6ce8802153f0908fc1654f30dc472de41f106d9eb44 | Python | 8,042 | 182 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation... |
bdaca66515d9210130d5a2060bb2eeeee982576e8e0ab646747ae63c47e47420 | Python | 8,042 | 177 | import os
import subprocess
import argparse
import datetime
import time
import sys
import fnmatch
import re
#!!!!NEED TO RUN: source /groups/branson/bransonlab/mayank/venv/bin/activate AT COMMAND PROMPT BEFORE RUNNING THIS SCRIPT!!!!!
#base_dir ='/groups/branson/bransonlab/mayank/stephen_copy'
cut_off = time.mktim... |
315f10bff9f4b1b183011ca6c65cf53dc0326711fe98bea94ac72e099cc1a852 | Python | 8,043 | 145 | ## -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Imports
# -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
import copy
import os
import scipy.io
import numpy as np
import pandas as pd
from Functions.f_EEGPowerAnalysis import *
from Functions.f_AnalysisFunctions import *
import ... |
35175f45a1e19de203375a7f85b011965b2e7c792b58c3f9dc91362bd11991b1 | Python | 8,046 | 230 | import os.path as osp
import numpy as np
import torch
import pandas as pd
from torch_geometric.data import InMemoryDataset
from torch_geometric import data as DATA
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
import networkx as nx
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit ... |
9d3ca3c7a8821194d00feaf74551faa8593edb43db66613aeea73a6e76784652 | Python | 8,046 | 264 | # 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... |
ba25c31de2f2585c6e7ac9411ffe22177f540a80230e5c87f890fca709ee15e1 | Python | 8,046 | 188 | import numpy as np
import cv2
from typing import Tuple
from merlin.core import analysistask
ExtentTuple = Tuple[float, float, float, float]
class GenerateMosaic(analysistask.AnalysisTask):
"""
An analysis task that generates mosaic images by compiling different
field of views.
"""
def __init_... |
eb340e3d939014ef6a7c2ad31d538708c0a227a1a971b69998e5223f0b8e2090 | Python | 8,046 | 176 | """
FEATHER_PASS_E_FULLSCALE.py
Full-scale replacement for FEATHER_PASS_D_RANDOM.py + /tmp/ess2.py.
Instead of a random 4,000-segment sample it runs the effective-sample-size
correction over EVERY FlyWire mat571 segment with n >= 100 synapses
(126,419 segments, 120,588,207 synapses = 92.7% of the brain).
Method is a ... |
6b82e0ef1d27d177b33e3f177dd1eb4f61f252e19379d93b0e1dedbb33734ff8 | Python | 8,049 | 153 | # coding=utf-8
# Copyright 2021 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 applicable... |
edb6ddac297ebaec4e461464415d85163be8f0bf823095ce03b60c01857959a0 | Python | 8,049 | 206 | """Holder for and manipulation of search results."""
import re
from hed.errors.exceptions import HedQueryError
from hed.models.query_expressions import (
Expression,
ExpressionAnd,
ExpressionDescendantGroup,
ExpressionExactMatch,
ExpressionNegation,
ExpressionOr,
ExpressionWildcardNew,
)
f... |
f36038532208dcfe24f1d145c20914d2a664630912c8c5570f9416564c586e18 | Python | 8,052 | 190 | """
Classes for expressing a DisPerSe skeleton as a graph
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
"""
__author__ = 'martinez'
try:
import pickle as pickle
except:
import pickle
from .core import *
############################################################################... |
f45aa6c7bda638be50d25d4d64e6d63fa7f31f97cf3e77fc4cb1132449d6083e | Python | 8,053 | 227 | #
# 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 ... |
230b12fecb7c9d220baba3cceaa34937b377262fa76bad4ab68e57aaf1189048 | Python | 8,057 | 240 | import numpy as np
import pandas as pd
import pytest
from lifelines import WeibullAFTFitter
from SurvivalEVAL.evaluations.calibration.single_time import one_cal_ic
from SurvivalEVAL.evaluations.prediction_error import inclusion_rate, mean_error_ic
from SurvivalEVAL.evaluators.interval_cen_evaluator import IntervalCenE... |
b8ceadb6300f0675faf790897eac15ca25f71b57edb58b01d4ba83a5e8060067 | Python | 8,057 | 245 | import numpy as np
import torch
import math
def get_regions(pooling_fun,img_size,nClass,shrink_maxsz):
if(pooling_fun == "2d"):
regions = split_regions_2d(img_size,nClass,shrink_maxsz)
elif(pooling_fun == "2d_edge"):
regions = split_regions_2d_edge(img_size,nClass,shrink_maxsz)
eli... |
46aca85d9be4bab96d85cc2a5fa1b1b390c630aa39a6141b5db1a8114787a995 | Python | 8,059 | 159 | # coding=utf-8
# Copyright 2021 Google Research and The HuggingFace Inc. team. 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/LICE... |
30fa767e2c0b790280228306e9fd8ec71199eda7a8aae6d8e2d1ad0a5d47df10 | Python | 8,061 | 220 | """
Created on 27/07/2020
:author: Chinchien Lin
:summary:
"""
import datetime
import json
import os
import sys
from functools import cmp_to_key
from src.segmentation.multichannel_segmentation import MultiChannelSegmentation
class MultiSliceSegmentation(object):
"""
Perform multi-slice im... |
582f8521f384d4b07dd51112254530b972cec5466a8228e5b17845728cc824d4 | Python | 8,061 | 165 | from cooler.create import ArrayLoader
import h5py
import cooler
from Bio import SeqIO, motifs
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
import matplotlib.pyplot as plt
import matplotlib
from scipy.ndimage import gaussian_filter
from torchmetrics.image.fid import FrechetInceptionDistance... |
e31dbe0bcc1dee4b61815078e4fd08fa8ba849ee089df6f406ee917a9f739649 | Python | 8,061 | 153 | #!/usr/bin/env python
import os
import numpy as np
import pandas as pd
from scipy import io as sio
## where are matrices located?
projpath = os.path.join('/project', '3011157.03', 'Simon', 'proj_2022_CABB_movie', 'DistanceMatrices')
## where should new matrices be stored?
dir_out = os.path.join('/project', '3011157.03... |
16e963633d9a167088f2e05edf902ffbfaabe7331b1fa6315a705ee5c421a91e | Python | 8,062 | 233 | #
# 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,... |
5778a52ec172d8f6298c679a0ab36edacd168f0488ba113ac55e47288a3d93c7 | Python | 8,062 | 201 | """Column sources: what tabular validation asks of a table, independent of how the table is stored.
The staged tabular validator (:class:`~hed.validator.spreadsheet_validator.SpreadsheetValidator`) never
reads a table directly. It asks a column source for the column names and for the distinct values of one
column at a... |
9333ce98a7782abb77ba8bca574422501963ff80224203d08ef8397196c55229 | Python | 8,064 | 219 | """
version 1.0
author: Felix Plasser
description: Procedures for plotting using the Matplotlib/pylab interface.
"""
import os, sys
import numpy
import pylab
import file_handler
def mean_std_from_files(mean_file, out_dir, xlist, std_file=None, col_list=None):
"""
Makes a number of mean/std plots from a file c... |
6fc9d40104c598c148543d02f3712e316bf1aa09bad00dafb352b654fbe03598 | Python | 8,066 | 241 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Some plottin' functions used by the example scripts
Copyright (C) 2017 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 Fo... |
e3e99576b53fac7bb7bc5fea9c575b4e62a771474a50ae818d9f4942829c9da1 | Python | 8,066 | 249 | """Transition state recipes for Q-Chem."""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from monty.dev import requires
from quacc import job
from quacc.atoms.core import perturb
from quacc.recipes.qchem._base import run_and_summarize_opt
from quacc.recipes... |
d5c77585b39f2ffb15e45843db533bb98a0c0249f85cffef4ac09555d1cbd502 | Python | 8,069 | 202 | # 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... |
0d27c9256316061070edcc846cbc6ebf130395d7c8da348eed29e31af1251a1a | Python | 8,072 | 142 | """This script visualises the POM considered for the inference of repolarisation properties from the T wave"""
import os
from warnings import warn
import math
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from io_functions import export_ensight_timeseries_case, read_dictionary, save_panda... |
39bd28981e0e9596577c542d6a5568218e82808ace903e5865f01362fd835d98 | Python | 8,072 | 243 | """distutils.dir_util
Utility functions for manipulating directories and directory trees."""
import os
import errno
from .errors import DistutilsInternalError, DistutilsFileError
from ._log import log
# cache for by mkpath() -- in addition to cheapening redundant calls,
# eliminates redundant "creating /foo/bar/baz"... |
793ba79baf0e933b465b4ee99a6cd1daf7501d7265a81fb56e004c1fb26fc055 | Python | 8,073 | 253 | #
# 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,... |
265517387baf44eaa639a1ed119b29f2b7e913b78e0c21a062c37bd06ee04209 | Python | 8,074 | 254 | """Kfold crossvalidation class.
Class
-------
KFoldCV
"""
import multiprocessing as mp
from copy import deepcopy
import numpy as np
import xarray as xr
from hmp.patterndata import PatternData, select_indices
from hmp.utils import _define_random_state
class KFoldCV:
"""
K-fold cross-validation for HMP Eve... |
855ab120b7f329034de0d38602b83519860df7f52069d0ca9a29ef195dfe6204 | Python | 8,075 | 180 | import torch
import torch.nn.functional as F
from utils import load_dataset, feature_generator, adj_polynomials, l2_reg_loss, cluster_infer, cluster_number, \
to_sparse_tensor
from sampler import get_edge_sampler
from model import PolyGCN
from loss import BerPossionLoss
from sklearn.decomposition import TruncatedSV... |
d55c9715279b4c364ff5680dc332a640fbc7fbd6402d774303ec7ffab895439a | Python | 8,075 | 178 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 12 13:31:38 2023
@author: caroline
"""
import argparse
import sys
import scipy
from scipy.stats import spearmanr
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
import seaborn as sns
from sklearn.linear_model import ... |
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