sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e6ffdc7041af499123e2f5c18116b16e3e2d12531bf39e02670d6becb8e94a6b | Python | 28,451 | 800 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import os.path as osp
from abc import abstractmethod
from dataclasses import asdict as dataclass_asdict
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from tempfile import NamedTemporaryFile
from urllib.parse... |
2dde056fd6f5d1cd5ef92eea223088e180c62280c6dffe09d8ff21504d99e00c | Python | 28,456 | 817 | import json
from collections import Counter
from collections.abc import Generator, Iterator, Sequence
from copy import copy
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any, Union
import torch
import torch.nn.functional as F
from aislib.misc_utils import ensure_path_exists
from torch.utils.data ... |
566641cba63d786a3aa2edfd275cb81d5b8aab2dcd7fb3153572c41695393212 | Python | 28,465 | 648 | # -*- coding: utf-8 -*-
"""
Created on Sat Jun 29 00:23:18 2024
@author: aka2333
"""
#%%
%reload_ext autoreload
%autoreload 2
from itertools import permutations, product
import time
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import numpy as np
import pandas as pd
... |
25956add5e2af0a2d95827e0698950052b7e42c161fbfb28c3533715f68ac12d | Python | 28,466 | 847 | from __future__ import annotations
import asyncio
from collections.abc import Callable
from typing import TYPE_CHECKING, Any, get_type_hints
try:
import ipywidgets
from ipywidgets import widgets as ipywdg
except ImportError as e:
raise ImportError(
"magicgui requires ipywidgets to be installed to ... |
de7055d6dc8307168dd183033ca2ed8785ee8092aece020f04321ff061ab0f24 | Python | 28,478 | 735 | """
Defines the controller UI
"""
import typing
import asyncio
import datetime
import functools
from ..qt import *
import numpy
from ..util import MeteredUpdater
from .task_context import TaskContext, TaskDescription
from .util import remove_by_is
from ..config import *
from .tasks import DESCRIPTIONS as TASK_DES... |
fee0ddee08fb83f460abbd09c2b541abea89aa267b53850bd00805feca17e515 | Python | 28,490 | 731 | #!/usr/bin/env python3
"""
This is to prepare the processed SSC samples for SFARI long-read sequencing data deposition. Currently only supports PacBio + Nanopore data
Usage: sfari_data_deposit.py --sample 11918_s1:SSC --proj_dir --ont_dtype fast5
Author: Mei Wu https://github.com/projectoriented
"""
import sys
if sys.... |
a56656a09c718d20a704c369ec0785cf654c2665992fff1a5626f15bed14c885 | Python | 28,494 | 997 | # -*- coding: utf-8 -*-
"""Mesh utilities."""
import datetime
import functools
import itertools
import os
from shutil import copyfile
import nibabel as nb
import numpy as np
from nibabel.freesurfer.io import (
read_geometry,
read_label,
write_geometry,
write_morph_data,
)
from numpy.linalg import norm... |
98d49a01e14c699353c20b38f66a57244f89a3373c5b872d6ae62e73cdeab137 | Python | 28,532 | 851 | import torch
from typing import Optional, Union, Dict, List, Any, Callable
from .scatter import scatter, scatter_softmax
from torch_geometric.nn.inits import glorot
from mlcg.nn import MLP
from mlcg.nn._module_init import init_xavier_uniform
from mlcg.nn.painn import PaiNNInteraction, PaiNNMixing
from mlcg.nn.so3krate... |
2899392924112b9cca152aafdb20c7afbec1d047a47bcc2401ee4a44ec5fb5d2 | Python | 28,552 | 753 | #Lucas Sancéré -
import json
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import plotnine
import seaborn as sns
import yaml
from attrdictionary import AttrDict as attributedict
from plotnine import (
aes,
geom_density,
ggplot,
labs,
scale_color_manual,
scale... |
6c04104bbcb84ecfe2c6619f9213abaf9291c13d57443492f85c7645cb4795a1 | Python | 28,578 | 712 | from infopath.session_stitching import build_network
from models.pop_rsnn import PopRSNN
from datasets.prepare_input import InputSpikes
import numpy as np
import torch.nn as nn
import torch
from infopath.utils.logger import optimizer_to, reload_weights
import os
import copy
from geomloss import SamplesLoss
from infopat... |
089095eb02bb066611008fad13dfba14ff971f61f7aad9e29ef6c83a255d9470 | Python | 28,591 | 790 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publi... |
dccd53bea645b379d500adfd1a9ca5031d00d4ee52a13d8fbbe8e3ee74df3f6c | Python | 28,592 | 807 | import glob
import pickle
import numpy as np
import pandas as pd
from os import path
from nilearn._utils.niimg_conversions import check_niimg
from nilearn.glm.first_level import FirstLevelModel, make_first_level_design_matrix
from nilearn.image import get_data
from nipype.interfaces.base import (
BaseInterface,
... |
d3de9cc0aa0c1f2c0b17c28ea35d1ae971ae7b56f1b7a5c2e3513e5b45e5efaa | Python | 28,622 | 593 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""
Run prediction on images, videos, directories, globs, YouTube, webcam, streams, etc.
Usage - sources:
$ yolo predict model=yolo26n.pt source=0 # webcam
img.jpg ... |
5f30235eff63ca4e842f69e90fa8829c1d365483527ed80f83cf6974e0aee127 | Python | 28,640 | 703 | """
Unified Feature Extraction Script - For Research Reproducibility
This script extracts feature vectors from three different data sources:
1. Binder Features: Extract 65-dimensional features for matched ImageNet classes from CSV
2. Concept Vectors: Extract concept vectors from multiple .pt files (30 trails, 20-dim v... |
0dfe2e978e8238a3e587be614d0215f8f83c4b8f8b56031b4009a271ceacb678 | Python | 28,641 | 625 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import os
from pathlib import Path
from typing import Any
import numpy as np
import torch
import torch.distributed as dist
from ultralytics.data import build_dataloader, build_yolo_dataset, converter
from ultralyt... |
91dd91c763be297c00980c5972aaec9ce31b8a1036fa786170e3cf8ae62af643 | Python | 28,649 | 641 | import torch
# from torch.optim.lr_scheduler import StepLR
from .dataset import SpatialOmicsImageDataset
from .net import SparseNet_Grand,SparseNet
from ..visualization.visualization import vis_scatter_label
from sklearn.metrics import adjusted_mutual_info_score
import os
import numpy
import datetime
import csv
from tq... |
0e1ece4fbc46a60495108db4b30fa275f2bae0aee64882489a09ae91583a874c | Python | 28,650 | 885 | import numpy as np
import numexpr as ne
from nems.registry import layer
from nems.distributions import Normal
from .base import Layer, Phi, Parameter
from .tools import require_shape, pop_shape
from nems.preprocessing.normalization import log_compress
class StaticNonlinearity(Layer):
"""Apply a nonlinear transfor... |
0091f91bd6c28f43731d9363962070bd423283d35d54d0afac6aae8e0d6e503d | Python | 28,745 | 607 | import copy
import numpy as np
# 3x3x1 grid of fODF taken from the outside of the backwards 'C'
# in the FiberCup. Order 8, descoteaux07 basis.
fodf_3x3_order8_descoteaux07 = np.asarray([[[
[0.26286387, -0.336828, -0.00369634, -0.25474626,
-0.01061569, 0.29750797, 0.03732642, 0.01171304,
0.16143565, 0.0... |
daa596dd1befa3e27a0c636f5d9696edae11cc8beef288a1bc2357d6b7108f4d | Python | 28,757 | 942 | import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import pandas as pd
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from sklearn.metrics import auc, r2_score
from scipy import stats
from scipy.odr import Model, Data, ODR
def AIF_fit(
t,
AIFm,
RETURN_FIT... |
a2b09197e582b7ce8db6590b5508a90953f243dde1f00dd11237968caf59ca39 | Python | 28,763 | 704 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
e3b7033d49832a640a61c1db8dfcedd38d80183623ceaf63c8f9e2838189b3fa | Python | 28,769 | 648 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""Postprocessors class to transform MDETR output according to the downstream task"""
import dataclasses
import logging
from collections import defaultdict
from typing import Dict, List, Optional
import numpy as np
import torch
from sam3.model ... |
1c24948fcd529f2ea36f2ad5f0a186bb22475d363598efbf8fc4c31f905bd9e8 | Python | 28,780 | 660 |
"""
Elastix registration plugin for Lasagna
Rob Campbell
"""
import os
import shutil
import subprocess # To run the elastix binary
import tempfile
from PyQt5 import QtGui, QtCore, QtWidgets
from lasagna.plugins.lasagna_plugin import LasagnaPlugin
from lasagna.plugins.registration_plugins import elastix_plugin_UI... |
1b31f8a3c6fb5c18d65dd5e769667a3aee9e5055dd706d9ed3a9d15da38234e1 | Python | 28,799 | 744 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from dipy.core.gradients import gradient_table
from dipy.core.sphere import disperse_charges, HemiSphere
from dipy.reconst.dti import fractional_anisotropy, mean_diffusivity
from beltrami import (fraction_init_s0, fraction_init... |
425e289bbefa18eb07ad8c8c2a5a324a2587c679e130462c90a329d566d9cd8f | Python | 28,808 | 743 | """
Wrappers for the TORTOISE programs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"""
import logging
import os
import os.path as op
import subprocess
import nibabel as nb
import nilearn.image as nim
import numpy as np
import pandas as pd
from nipype.interfaces import ants
from nipype.interfaces.base import (
BaseInterfac... |
86c7e96ad49fbb47fdeb7610616a6f4e623aebb339a8cf63d2435169b7856c4b | Python | 28,816 | 442 | class W417():
"""
A class to store molecular data and corresponding calculations for W417 dataset.
Attributes
----------
molecules : list[str]
List of molecule identifiers used in test calculations.
exp_values : dict[str, float]
Dictionary mapping test identifiers to their expe... |
8ae1fbb2249afa6faac2e101e1eae323e2f23cb5525610f960a8157e02cd9c05 | Python | 28,833 | 692 | import torch
from torch import nn, einsum, broadcast_tensors
import torch.nn.functional as F
from einops import rearrange, repeat
from einops.layers.torch import Rearrange
# types
from typing import Optional, List, Union
# pytorch geometric
try:
import torch_geometric
from torch_geometric.nn import MessageP... |
6cf1b10ed16a1c7cb807b3c8cd348cb800b744cff75f36a855816ce59d6008fb | Python | 28,852 | 921 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import itertools
import logging
import os
import shutil
import unittest
import unittest.mock
from collections.abc import Callable, Collection, Generator, Iterator, Sequence
from contextlib import contextmanager
from copy import deepcopy
from io impor... |
aa3186dd0dd0e858c96eb6e83d4c63e37f899c5f06831cac48683d3b2b5ce8e4 | Python | 28,856 | 769 | # encoding : utf-8
# IO module for reading data from CRCNS hc-11
# Author: Etienne Ackermann
# Date: January 2019
"""This file contains nelpy io functions for reading data from hc-11.
See https://crcns.org/data-sets/hc/hc-11/about-hc-11.
datatype = ['spikes', 'lfp', 'pos', 'waveforms', 'metadata']
"""
# __all__ = ... |
eb5603cd1cbb12cb7c59f4fe84e41ef124f522241247559d5df48f4b36f66581 | Python | 28,884 | 615 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A class to load, parse, and control predefined kilroy protocols, i.e.
# collections of predefined valve or pump configurations and a defined
# duration to wait before setting the next configuration. This class... |
db39d6765a3c2f94092c2dde7ec554caa2ade0e24997e391bf553a8c59aa3de9 | Python | 28,886 | 555 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Kathrin Rack, Wadim Koslow, Martin J. Kuehn, Annette Lutz
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use ... |
e40aec6dddca29707da40e3f166510e509f7f9d9fa57d03ab6df908bf98815d2 | Python | 28,886 | 555 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Kathrin Rack, Wadim Koslow, Martin J. Kuehn, Annette Lutz
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use ... |
b06c529b8e03662fa33143d77725796f81435113e33fcdb90a3288d3b361cbf5 | Python | 28,916 | 803 | """Generator for 3d video images."""
import numpy as np
import tensorflow.keras as keras
import tensorflow as tf
import os
from tensorflow.keras.applications.vgg19 import preprocess_input as pp_vgg19
import imageio
from dannce.engine import processing as processing
import scipy.io as sio
import warnings
import time
imp... |
96db468a4b873c267018316b3d3fdf4a63939face228982e9978006a71edd439 | Python | 28,933 | 719 | """CLI configuration and error-handling regressions for Deep Agent."""
import io
import os
import select
import subprocess
import sys
import time
from types import SimpleNamespace
import pytest
import toml
from rich.console import Console
from chemgraph.agent.interrupts import PendingInterrupt
from chemgraph.agent.l... |
12d2bd7000cf105f651e51be45f1b172a0d644c8caca5c40f0c9ab12b396c24d | Python | 28,936 | 537 |
import pathlib
import time
import numpy as np
from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar
import matplotlib
from matplotlib.collections import LineCollection
import matplotlib.font_manager as fm
matplotlib.use('Qt5Agg')
import matplotlib.pyplot as plt
from helper_functions.get_dendritic_curren... |
21a8cab1ec642cf5bf34f4cf5c906891ed1ce56eaee3be8bed9b2e87768c66b0 | Python | 28,945 | 616 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A class to load, parse, and control predefined kilroy protocols, i.e.
# collections of predefined valve or pump configurations and a defined
# duration to wait before setting the next configuration. This class... |
ec14862b49885ee048d076b20f4d33edb3d8188efd0fa3d1ea689a6f4716abe2 | Python | 28,973 | 590 | import cv2
import numpy as np
from qtpy.QtGui import QImage, QPixmap
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view.DotObject import DotObject
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation import fitGeoTrans
from napari_dmc_brainmap.registration.sharpy_track.sha... |
5c615b635a9580fe7ab63601751ff947bdcc632b9d72d2a573c5470a44a10251 | Python | 28,982 | 619 | # Batch processing of cohorts with dmriprep
#
# A batch lives in its output directory:
# <out>/batch/batch.yml settings (config directory, dmriprep command, version)
# <out>/batch/manifest.tsv one row per dataset: id, images, output folder, protocol, overrides
# <out>/batch/prot... |
5db7fdf9db7dc8399ce51652eaa729098392200582f57cd5bb569b14cca89b84 | Python | 28,982 | 775 | # encoding : utf-8
# IO module for reading data from CRCNS hc-18
# Author: Etienne Ackermann
# Date: November 2018
"""This file contains nelpy io functions for reading data from hc-18.
The data set includes 5 sessions (i.e., 5 rats), each consisting of three travel
sessions (passive, active, passive; 2~15 laps each) ... |
25ce9663807ade92ecfe0a256d1a8e82adc2f388631a02ae1ce57f0e9819e71e | Python | 29,012 | 664 | import torch
import pandas as pd
import os
import os.path as osp
from datetime import date
import shutil
from tqdm import tqdm
import numpy as np
from ogb.io.read_graph_raw import read_binary_graph_raw, read_binary_heterograph_raw
from ogb.utils.torch_util import all_numpy
class DatasetSaver(object):
'''
A... |
8e4b805f16b6e8146d3bbe831187a72a2c20867234f8e680c2aed35aef7b7672 | Python | 29,031 | 631 | import numpy as np
import tensorflow as tf
import pandas as pd
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import f1_score, accuracy_score, confusion_matrix
from keras.utils import np_utils
import matplotlib.pyplot as plt
import scipy.stats as stats
from sklearn.calibration import calibration_cu... |
8d90c84b3f70b28fd55cb1faebec15cf43035b91f9afc132dafb956d77087325 | Python | 29,095 | 958 | # laminar_rs/schaefer_stats.py
"""
Schaefer-400 / RSN-7 network statistics with spatial null models.
This module provides:
- Bookkeeping for Schaefer-400 parcels on fs_LR 32k
- Safe parcel ↔ vertex mapping helpers
- Network-wise ANOVAs (per layer) with spin nulls
- Network × layer interaction tests with spin nulls
- S... |
2a1f8d212151c5ae256d69aa0461290c05e210747638b346246e21e42f82e0b5 | Python | 29,098 | 766 | import pdb
import numpy as np
import numpy.fft as fft
import time
import os
import json
from matplotlib import pyplot as plt
from scipy.signal import find_peaks, savgol_filter
import pandas as pd
from scipy import signal
from pybaselines.polynomial import imodpoly, modpoly
from scipy import integrate
from json impo... |
c128490aad1a9342cbdf1fad6d4c1dfc1bb63df48d296347b846de11a479aa01 | Python | 29,133 | 684 | # Required libraries
import matplotlib
matplotlib.use('Agg') # Set globally for all matplotlib usage
import os
os.environ['PYTORCH_CUDA_ALLOC_CONF'] = "max_split_size_mb:100"
os.environ['KMP_DUPLICATE_LIB_OK']="True"
os.environ['CUDA_LAUNCH_BLOCKING']="1"
import random
import glob
import time
import matplo... |
2436d1d42738f3dd2230690370dadf58380fdc10815a10a35b43d2059e0da4ac | Python | 29,164 | 858 | from __future__ import annotations
import dataclasses as dc
import sys
import warnings
from collections.abc import Callable
from dataclasses import dataclass, field
from functools import cache
from types import FunctionType
from typing import (
TYPE_CHECKING,
Annotated,
Any,
Generic,
Literal,
T... |
dfe986a3fdc706aa5f7d2a15aeadbb5735deeda0b521b92601373f1278eb36a1 | Python | 29,165 | 716 | # -*- coding: utf-8 -*-
"""
Globe Shape Analysis Pipeline for 3D Slicer
A modular, open-access tool for analyzing eyeball shape projections
from template space to subject space.
Features:
- Orthogonal and polar projection analysis
- Cross-platform path handling
- Configurable via dataclass
- Lazy Slicer integ... |
12e310d93dc5f07db5e75a42cba3012b2a29133ef3d524cc0245de9a82bb92ae | Python | 29,179 | 556 | import sys
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout
from superqt import QCollapsible
from napari.qt.threading import thread_worker
from magicgui import magicgui
from magicgui.widgets import FunctionGui
import numpy as np
import pandas as pd
from natsort import natsorted
from matplotlib.backends.b... |
9d2300e012c7d554284aef6ef1f9386df4fcbf08a78ec6f4b762cfae0459b349 | Python | 29,193 | 652 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import ast
import json
import unittest
from pathlib import Path
from types import SimpleNamespace
from unittest import mock
import datumaro as dm
import numpy as np
from attrs import evolve
from cvat.apps.dataset... |
f84552541d9680a1c0ffbfb8c2a6210eae0400ddbae3f195371d7c2b1a255fb4 | Python | 29,208 | 960 | from __future__ import annotations
import base64
import json
from pathlib import Path
from typing import Final
import numpy as np
import PIL.Image
import pytest
from PySide6 import QtGui
from PySide6.QtCore import QPoint
from PySide6.QtCore import QPointF
from PySide6.QtCore import Qt
from pytestqt.qtbot import QtBot... |
879bfae26435cc0ed76022f030308b468e722fe825f1a91690fc1b024aca5d58 | Python | 29,213 | 603 | # -*- coding: utf-8 -*-
import numpy as np
import sys
import os
import datetime
# In[]
# Create ABAQUS inp files
def create_inp(meshfilename, b_width_distribution, sx):
# In[]
#############Hyper Parameters#############
L0 = 7.83
n_node1 = 541
n_element1 = n_node1 - 1
Bond... |
8629e5488339da0901ffb0d98e9349bd4db201b4e00772a1a20542dc4ec9c4bc | Python | 29,224 | 759 | r"""
Vis multi dataset and their connection
"""
import random
import math
from typing import List, Mapping, Optional, Union
import scanpy as sc
import numpy as np
import pandas as pd
from anndata import AnnData
import matplotlib.pyplot as plt
import plotly.graph_objects as go
from .color import *
def get_color(n=1... |
9a9293f907f6d7290f1f9676a5820c0f5c4e35bf07c1f4858f0c2554d00ba14a | Python | 29,224 | 1,006 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
93b63c05a507463c320d8e659e833042223585600fc377f8f23b7583a879c14b | Python | 29,232 | 688 | import os
import csv
import glob
from tqdm import tqdm
from ogb import linkproppred
import torch
import torch.nn as tnn
from torch.utils import data as torch_data
from torchdrug import data, datasets, utils
from torchdrug.core import Registry as R
class InductiveKnowledgeGraphDataset(data.KnowledgeGraphDataset):
... |
9c1543ceb8e017fb89f2d1ecdd0a568dd858a556c843ebbc45212bb9fc15ac75 | Python | 29,232 | 554 | """Spike detection settings.
Thirteen settings, of which two decide what a run does: which thresholds, and
which method's spikes feed steps 2-4. A third, above them, decides whether the
nodes are electrodes or *sorted units* — spike sorting replaces the detectors
when it is on (see :mod:`meanap.pipeline.spike_sorting`... |
067f626887c4e0d5830d658ca82bc1799e1b216d528a5c7f3a5e423c90a589a4 | Python | 29,242 | 747 | import copy
import inspect
import warnings
from typing import Any, Dict, Optional, Tuple, Type, Union
import torch
from torch_geometric.data import Data, Dataset, HeteroData
from torch_geometric.loader import DataLoader, LinkLoader, NodeLoader
from torch_geometric.sampler import BaseSampler, NeighborSampler
from torc... |
756f446d0046f1d3d4572bd8d8599cc30fae0c1cc589fe83b6fdbc2b14fcb948 | Python | 29,255 | 502 | # -*- coding: utf-8 -*-
"""
Created on Thu Jan 28 14:34:30 2021
@author: nehas
"""
import numpy as np
import sys
import pandas as pd
pd.set_option('display.width', 1000)
pd.set_option('display.max_colwidth', 100)
import warnings
warnings.simplefilter("ignore")#, category=FutureWarning)
import glob
import os
print ... |
12dbb5238f082ea665d309436a946942375ab1fde68ec6e791b226a21d0d82fc | Python | 29,291 | 789 | #!/usr/bin/env python
# coding: utf-8
# In[ ]:
#!/usr/bin/env python
# coding: utf-8
"""
AGED Optimal K Selection Module
Automatic selection of optimal number of topics using multiple evaluation metrics
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import pandas as pd
fr... |
78baac6e73f525add5ad4afa801c8b1246db551d43d7566f54396633447c0803 | Python | 29,291 | 735 | '''
'''
#
# Adapted from MATLAB code written by S. Nishimoto (see Nishimoto, et al., 2011).
# Anwar O. Nunez-Elizalde (Jan, 2016)
#
# Updates:
# Anwar O. Nunez-Elizalde (Apr, 2020)
#
import itertools
import numpy as np
from .utils import (iterator_func,
log_compress,
sqrt_sum_... |
3f4deec977fd3441968a5d41ba00b45d77016ef9ca48940b4f939f481a26d122 | Python | 29,302 | 637 |
import os
import torch
import math
import warnings
import torch.nn.functional as F
import pandas as pd
import numpy as np
import scipy.spatial as spa
from torch_geometric.data import Data, Dataset, InMemoryDataset
from tqdm import tqdm
from scipy.special import softmax
from Bio.PDB import PDBParser, ShrakeRupley
from... |
3bb6b260bcb731127b8dfda0d67a3f73c54926e6e7c3585ae0b639cba5c33f3e | Python | 29,320 | 902 | import reprlib
from collections.abc import Generator, Iterable, Sequence
from copy import copy
from dataclasses import dataclass
from pathlib import Path
from typing import (
TYPE_CHECKING,
Any,
Optional,
)
import numpy as np
import polars as pl
from sklearn.preprocessing import KBinsDiscretizer
from tqdm ... |
07d4411c56d40999157c3bba69b747faa743eac1a8997f419923f3565a311980 | Python | 29,333 | 640 | """Step 1 by spike *sorting*: units, not electrodes, as the pipeline's nodes.
The detectors in :mod:`meanap.pipeline.spike_detection` give one spike train
per electrode. On a dense culture an electrode often hears several neurons,
and every later step then treats their pooled activity as one node. Sorting
clusters the... |
44a439b070fe397ff3d15f28a046a253cdd20a2ecd8caa3bcc7d6218202924bc | Python | 29,344 | 620 | #!/usr/bin/env python3
"""
Unified DeepSTARR DEGU Distillation Training Script
This script trains DEGU distilled models that learn to predict both Dev and Hk outputs
from DeepSTARR ensemble predictions, following the @DEGU_paper methodology.
"""
import argparse
import logging
import os
import sys
from pathlib import ... |
11fd9553f279a43bcb8f1f4669ca0ee6e3986abd977cbf62419aa1bb5cb23c70 | Python | 29,372 | 625 | import ANNarchy as ann
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import os
plt.rcParams.update({'font.size': 40})
plt.rc('axes', labelsize=30)
plt.rc('xtick', labelsize=20)
plt.rc('ytick', labelsize=20)
plt.rcParams["font.family"] = "serif"
plt.rcParams["mathtext.fontset"] = "dejavuserif"
... |
0b87e03f878b502ae0b65baa36c9e2ac48b743357b52d2de4b11deb290bb271c | Python | 29,387 | 671 | # wfield - tools to analyse widefield data - command line interface
# Copyright (C) 2020 Joao Couto - jpcouto@gmail.com
#
# 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 t... |
0726eb031fe76ad620b95a2b265801082028df3d31551531b88c31a86815348d | Python | 29,389 | 769 | # -*- coding: utf-8 -*-
"""
@JimHokason's translation of the Schafer Lab's skeletonization code.
"""
import numpy as np
# If you are interested to know why the following line didn't work:
# import scipy.signal.savgol_filter as sgolay
# check out this: http://stackoverflow.com/questions/29324814/
# Instead we use th... |
0c9d444547e3ad57e2e35e03f4282ab256ff6205ef719b05f53bacc07255a164 | Python | 29,427 | 922 | # -*- coding: utf-8 -*-
"""Spatial properties of image arrays."""
import copy
import os
import random
import re
import matplotlib.pyplot as plt
import nibabel as nb
import numpy as np
import pydicom
from nibabel.freesurfer.io import read_label
from numpy.fft import fft, fft2, fftshift
from numpy.random import shuffle... |
87c4b1c909bc6564ca1a15e74a36edcbdf5a0ac1ea92f59ff9b888742c20e5c8 | Python | 29,450 | 663 | from staticnet_analyses.base import *
from tqdm import tqdm
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.stats import pearsonr,kurtosis
from collections import Counter
from scipy.spatial.distance import pdist,cdist
import torch.nn as nn
from staticnet_experiments import configs
from neuro_data.stati... |
01a996f67b008eb29191548233ef8786ba4ea9a9283f08064262e025a934ff59 | Python | 29,469 | 694 | """The shared folder a multi-computer run goes through, and what is in it.
A shared run lives in one directory inside whatever folder the machines have
in common — ``<shared folder>/<run name>.meanap-shared/``::
Run1.meanap-shared/
shared_run.json what the run is: settings, recordings, who
... |
41363cbac0aa788564cb39c921b34dea666b049d60f72dcd8e682b69c8928c91 | Python | 29,475 | 907 | #!/usr/bin/env python3
#
# This script converts between 2 model formats
# Formats are guessed from the suffix.
# All models are first converted to CARP format which is 0-index based
import sys, gzip, pdb, time, shutil,re
import os.path
import argparse
import numpy as np
import scipy.io as io
import struct
import meshi... |
446a401d019ee2196ba0e5e74d341ed5e92571fd06ae140b021d6b005583a1ba | Python | 29,481 | 777 | """
ECG datasets to use with ECGx.AI package.
MB Vessies and RR van de Leur
"""
import os
import torch
from torch.utils.data import Dataset
from scipy import io
from sklearn.model_selection import train_test_split
import numpy as np
from typing import List, Union, Callable
import pandas as pd
from torchvision.transfo... |
320ac16b50a8207a660b1921d66a944784d1ed8237635b9dc2be348de11b54b2 | Python | 29,510 | 704 | '''
Generate retina
-------------------
Functions to generate a retina parameter array defining a synthetic retina
and containing the ground truth data.
'''
import numpy
import os
import sys
from scipy.special import erf
from ERICA import ERICA_toolkit, peak_detection
####################
# GLOBAL VARIABLES #
####... |
7cf2d435918695d330821e0f182104f4af6a34e94d72e4a68bc870c99ddd6334 | Python | 29,537 | 600 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from collections import deque
from functools import wraps
from typing import Any
import numpy as np
import torch
from ultralytics.utils.metrics import bbox_ioa
from ..utils import LOGGER
from .basetrack import Tr... |
16a56bfe892a02e4c5a2f6402f330b1c0e6c2fe941f8dab7fc4c6a4bcd3820e3 | Python | 29,564 | 722 | """Network viewer panel: load a MEA-NAP output .mat file and plot the network."""
from __future__ import annotations
from pathlib import Path
import numpy as np
from PyQt6.QtCore import Qt, QThread, pyqtSignal
from PyQt6.QtWidgets import (
QComboBox, QDoubleSpinBox, QFileDialog, QFormLayout, QGroupBox,
QHBox... |
d9d382790650ebbbc2116fb6936c199a07abc04507799a5972f3753bb3b7f834 | Python | 29,590 | 569 | # YOLOv5 YOLO-specific modules
import argparse
import logging
import sys
from copy import deepcopy
from pathlib import Path
sys.path.append(Path(__file__).parent.parent.absolute().__str__()) # to run '$ python *.py' files in subdirectories
logger = logging.getLogger(__name__)
try:
from models.common import *
... |
a5aef51bf41f6898b2016f4d17e52d89122964f7ca6945995ee16362bf467746 | Python | 29,595 | 768 | """
tensorflow/keras utilities for the neuron project
If you use this code, please cite
Dalca AV, Guttag J, Sabuncu MR
Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation,
CVPR 2018
Contact: adalca [at] csail [dot] mit [dot] edu
License: GPLv3
"""
import sys
from ext.neuron import... |
aecfc34b9e670fa505fef997efbf30d6732957b7a2c276c2fcb5d9290ed5af98 | Python | 29,629 | 835 | # -*- coding: utf-8 -*-
#
# sampler.py
#
# Copyright 2020 Amazon.com, Inc. or its affiliates. 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... |
c33dcf3fa8de1e49ae931093cddd8dfc7ed206799ab143911741b86640d4a8e6 | Python | 29,646 | 817 | """
SettingsManager: Centralized manager for the settings/ directory.
Owns all file I/O under ``<dataset>/settings/``:
* **Geometry** – center, rotation, auto-geometry cache, global base
* **Flags** – transform, ignore, image-diff cache
* **Blank / mask state** – enable/disable flags, blank config JSON
* **Calibratio... |
a2d9f1c1e754710f9ddee2f51fcbc15f0892897babd5a02ca8bb6e0c4f659eca | Python | 29,667 | 505 | # -*- coding: utf-8 -*-
"""
This script performs the encoding model fits for all the sessions included in
the analyses.
Created on Mon Feb 10 00:11:53 2025
@author: Lukas Oesch
"""
import numpy as np
import pandas as pd
import glob
from os.path import splitext, join
import itertools
from labdatatools import *
from s... |
f1b9ab009c41093c0da0b8df890d0ba6705078e4f7c26269fdcf1182b621a678 | Python | 29,674 | 619 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Hyperparameter tuning for Ultralytics YOLO models across all supported tasks.
Hyperparameter tuning is the process of systematically searching for the optimal set of hyperparameters
that yield the best model performance. This is particularly crucia... |
3376a671c5e16d86fb67b87246bec4d91734900ca1610dab2ec85b3118e466ad | Python | 29,686 | 704 | import numpy as np
from monai.data import GridPatchDataset, DataLoader, PatchIter, PatchDataset, Dataset
from monai.transforms import RandShiftIntensity, RandSpatialCropSamples, Compose, RandFlipd
import SimpleITK as sitk
from typing import IO, TYPE_CHECKING, Any, Callable, Dict, List, Optional, Sequence, Union
from to... |
0381b5a2177dd2dfa014f5a720df43f7352738da1bd2bb59d11a4c6aca251d33 | Python | 29,714 | 574 | # YOLOv5 YOLO-specific modules
import argparse
import logging
import sys
from copy import deepcopy
from pathlib import Path
sys.path.append(Path(__file__).parent.parent.absolute().__str__()) # to run '$ python *.py' files in subdirectories
logger = logging.getLogger(__name__)
try:
from models.common import *
... |
54300d09ba065b026a32231b3ddedbfc9ad75194cd2b719a70bc22b079d6f36a | Python | 29,714 | 939 | import gc
import numpy as np
import pytest
import time
import torch
import xdas
from xdas import Coordinate, DataArray
from scipy.signal import resample_poly, sosfilt_zi, sosfilt
import seisbench.models as sbm
def test_get_n_patches():
patching_structure = sbm.PatchingStructure(
in_samples=500,
i... |
dd1379747784e6f74fe4429c062caef37e494cf4369f4bc4d4a02d9a3bd88691 | Python | 29,751 | 872 | #!/usr/bin/env python
import math
import sys
from numpy import (
float32,
putmask,
shape,
zeros,
)
# This is the average of all species in the alignment outside of exons
# > mean(r)
# A T C G
# 0.2863776 0.2878264 0.2129560 0.2128400
# > sd(r)
# ... |
98ea536adb7f07f794217e3ed2bc994dae8f7c1bce839cd7c6f959f61f2d88f7 | Python | 29,764 | 771 | """
XGBoost Regression Constraint Model for PFAS Resistance Prediction
=================================================================
This module implements an XGBoost regression model as a constraint model
for predicting initial resistance values in PFAS soil treatment systems.
"""
import pandas as pd
import nump... |
44cc6e8d7479ebf832aff06351c010676ad8a1201a6c04d60ba2b5039add9c90 | Python | 29,765 | 805 | import re
import bz2
from argparse import Namespace
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.distributed as dist
from torch.distributions import Normal
from torch_scatter import scatter_add
from torch_geometric.nn import global_add_pool
import dgl
import numpy as np
from scipy.sp... |
cf7879284e2702988d6429bd884691bd93d98b3f2e40df0dee6ff9a2d6392f7d | Python | 29,769 | 725 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Sascha Korf, Patrick Lenz
#
# 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 compliance w... |
cca036a1922faffd4077a6cbb2dffcd462c0037c62d11235bacfcbb6f7fd0aba | Python | 29,785 | 890 | """Module to generate networkx graphs."""
from jarvis.core.atoms import get_supercell_dims
from jarvis.core.specie import Specie
from jarvis.core.utils import random_colors
import numpy as np
import pandas as pd
from collections import OrderedDict
from jarvis.analysis.structure.neighbors import NeighborsAnalysis
from j... |
eec91ec6170d29fdcad5b8c94f9ee1e83e26bf4b8f20ac83ccacf3038e3ae2f4 | Python | 29,839 | 612 | import pandas as pd
import numpy as np
import json
from pathlib import Path
import random
from skimage import measure
from scipy.ndimage import zoom
from skimage.transform import resize
from scipy.ndimage import gaussian_filter
from scipy.spatial.distance import cdist
from sklearn.preprocessing import MinMaxScaler
impo... |
edd956fbefda4057cd75e4ff75b80ed9d5b8acfe525b06364e90af9298ec8978 | Python | 29,847 | 757 | """
This file contains several helper functions to calculate spectral power from
1D and 2D EEG data.
"""
import logging
import mne
import numpy as np
import pandas as pd
from scipy import signal
from scipy.integrate import simpson
from scipy.interpolate import RectBivariateSpline
from .io import set_log_level
logge... |
b9e86f1bae39d99e15388ff3412fe94a2628a9930960b6c85fb44bdf1061e1ba | Python | 29,875 | 1,084 | """circstats.py -- circular statistics module
This software is licensed under the terms of the MIT License as
follows:
Copyright (c) 2013 Jessica B. Hamrick, Peter W. Battaglia
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Softw... |
26f99fcdd619ff1a7a2eda55d5f12727cbc83725e471fc8086711fbc0c1cfa55 | Python | 29,916 | 846 | """Simulation data loading functionality."""
import os
import numpy as np
import pandas as pd
import torch
from mcmlnet.data_gen.camera_adaptation import adapt_simulations_to_tivita
from mcmlnet.experiments.data_loaders.config import DataConfig
from mcmlnet.experiments.data_loaders.utils import (
subsample_data,... |
d24e5683bfd6037feedd5ef9713b6f0a92fba0b50f52ea8277190908dbeb9184 | Python | 29,919 | 817 | """Shared chemistry-screening helpers for scripts/demo/*.
Each demo script in this directory is a thin wrapper around
``submit_and_collect`` -- the actual chemistry workload (a 5-molecule
thermochemistry screen) lives here so we don't duplicate it across
backends.
Workload
--------
For each of {water, methane, ammoni... |
b5f29c9a8f6042117d8ffca32fba027c882c13658e232237f8faf24b1c3e72f3 | Python | 29,930 | 932 | #!/usr/bin/env python
"""
Handles parsing settings xml files and getting/setting
the resulting settings.
Hazen 06/15
"""
import copy
import os
import traceback
import xml
from xml.dom import minidom
from xml.etree import ElementTree
#
# Functions.
#
def config(config_file):
"""
Parse... |
9ba6a867eb21c9b4bac0e7edb8931af5e414a8c2b030bc45cd238aa5d0a377ec | Python | 29,971 | 899 | """Tests for the middleware-based main-agent supervisor."""
from typing import Annotated, Any, NotRequired, TypedDict
import pytest
from deepagents.backends import LocalShellBackend, StateBackend
from deepagents.middleware import SubAgentMiddleware
from langchain.agents import create_agent
from langchain_core.languag... |
36eaf2d0cee7479f239504ec8347fad5be648b505de41b7b8f99178aa36c8b0f | Python | 29,972 | 662 | # ========================
# 📦 Imports & Setup
# ========================
import ast
import io
import pandas as pd
import plotly.io as pio
import streamlit as st
import yaml
try:
import altair as alt
alt.data_transformers.disable_max_rows() # prevent silent failures on larger data
except Exception:
pas... |
d0b93675d6e4b0d125111e055910e5897d1de5fd6e6c25bf7c6bd57465346cc0 | Python | 29,973 | 752 | # -*- coding: utf-8 -*-
from contextlib import nullcontext
import itertools
import logging
import multiprocessing
import os
import sys
from tempfile import TemporaryDirectory
import traceback
from typing import Union
from tqdm import tqdm
import numpy as np
from dipy.data import get_sphere
from dipy.io.stateful_tracto... |
059aee4f783e8cb02655f393d9ecb5a8ca2fabf0ee64615b319b518166d6b1b7 | Python | 30,014 | 818 | # Copyright (C) 2020-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import io
import itertools
import math
from abc import ABCMeta, abstractmethod
from bisect import bisect
from collections import OrderedDict
from collections.abc import C... |
72b9070f28c19f2dead793a0b2e3d1ddad58c622448f66c209d3cc21934f0f95 | Python | 30,028 | 888 | # 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, sof... |
40618c32c978a9bfb029aca5e6c64f878e1f357ef1d9c8e910d9b22990f5746a | Python | 30,046 | 622 | from qtpy.QtCore import Qt
from qtpy.QtGui import QPixmap,QColor
from qtpy.QtWidgets import QWidget,QStackedLayout,QPushButton,QVBoxLayout,QHBoxLayout,QLabel,QMainWindow,QMessageBox,QTableView,QDialog,QDialogButtonBox
from qtpy import QtGui
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view.AnchorRow ... |
4ca5b15ce4f792339131dff400fea79a2e9caf60ffa371d1250d3ab64f329551 | Python | 30,050 | 622 | from PyQt5.QtCore import Qt
from PyQt5.QtGui import QPixmap,QColor
from PyQt5.QtWidgets import QWidget,QStackedLayout,QPushButton,QVBoxLayout,QHBoxLayout,QLabel,QMainWindow,QMessageBox,QTableView,QDialog,QDialogButtonBox
from PyQt5 import QtGui
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view.Anchor... |
657c2e20277d106485f677bde408f46b01e3d03ff8d9a472417ac0879d53f565 | Python | 30,053 | 698 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
from collections import Counter
from contextlib import closing, suppress
from copy import deepcopy
from django.db import transaction
from django.db.models import OuterRef, Subquery, prefetch_relat... |
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