sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ad0bb729ac589b7fb3412a8adba059c2b3d87312ecb08392f312307eba9e176d | Python | 13,717 | 443 | """ Test mesh operations """
import pytest
import os
import numpy as np
import shutil
import gzip
import vtk
from vtk.util.vtkConstants import VTK_TRIANGLE, VTK_LINE, VTK_VERTEX
from brainspace.vtk_interface import wrap_vtk
from brainspace.vtk_interface.wrappers import BSPolyData
from brainspace.mesh import mesh_io... |
668dc02b847c7fc7ae3d8d35c4421af4dfd860b324b41b73f1b249a23e85d250 | Python | 13,718 | 292 | import scanpy as sc
import numpy as np
import pandas as pd
import os
from sklearn.neighbors import kneighbors_graph
import datetime
from typing import Optional
def formulate_HRCHYCytoCommunity_input_from_anndata_singlecell(adata,sample_id,ct_col,categories,
... |
75646d37c69dce0fe31cb66334371e8470f69efa21ede145498d6301dcf22e76 | Python | 13,727 | 331 | #!/usr/bin/env python
# coding: utf-8
import os
import random
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset
from torch_geometric.nn import GCNConv
from tqdm import tqdm
from sklearn.model_selection import StratifiedKFold
from skl... |
139e86a1cdd1266d7b54eda0a81d10c6c03c748d5ba809e7b982cda154c71905 | Python | 13,728 | 295 | # -*- coding: utf-8 -*-
#
# utils.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.org/... |
927c80fcc47e6ad78b6369bed1426e56eaeb6e38f5b47d156321e6e976fb0534 | Python | 13,728 | 302 | #!/usr/bin/env python
"""
The stage GUI.
Hazen 04/17
"""
import os
from PyQt5 import QtCore, QtGui, QtWidgets
import storm_control.sc_library.parameters as params
import storm_control.hal4000.halLib.halDialog as halDialog
import storm_control.hal4000.halLib.halMessage as halMessage
import storm_control.hal4000.hal... |
4537a542e0a2278c11f8f51f5a11f87f34058041592557e0b9fbb9ac6101ed4a | Python | 13,735 | 338 | import pickle
from pathlib import Path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from PIL import Image, ImageDraw, ImageFont
from sklearn.calibration import calibration_curve
from sklearn.metrics import confusion_matrix
from config.config import settings
from evaluati... |
534c9cf6778d658b067ffb1858ef917603ed90f70cf46cb04f59a1ffe1b3a06a | Python | 13,742 | 509 | import os
import gzip
from dataclasses import dataclass
from typing import List, Tuple, Optional, Dict, Any
import numpy as np
from scipy.io import loadmat, savemat
@dataclass
class TinyTrackData:
streamlines: List[np.ndarray]
dimension: np.ndarray
voxel_size: np.ndarray
metadata: Dict[str, Any]
de... |
8be0331aaa29af37660f81954a52bcc92dd08424656e505a87d4cbcaa405d5d6 | Python | 13,742 | 440 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import re
from collections.abc import Sequence
from enum import StrEnum
from pathlib import Path
from types import NoneType
from typing import TYPE_CHECKING, Any, ClassVar, TypeAlias
from attrs import frozen
from ... |
c1295d88ad7f9dc9651463834e06268b2cca53883bfd24922c6ff9fda7cf5743 | Python | 13,745 | 405 | """EnsembleLauncher execution backend.
Wraps `EnsembleLauncher <https://github.com/argonne-lcf/ensemble_launcher>`_
to conform to the :class:`ExecutionBackend` interface. Uses the
cluster-mode API (``EnsembleLauncher.start()`` + ``ClusterClient``) so
that tasks can be submitted dynamically.
EnsembleLauncher must be ... |
92bb63188e163c9ff18b509f71cc6ffa85f5a1a31e4c4efa85da89cc2fc6a1b8 | Python | 13,748 | 310 | import os
from pathlib import Path
from argparse import ArgumentParser
import json
import numpy as np
from tqdm.auto import tqdm
from brainscore_core.supported_data_standards.brainio.assemblies import NeuroidAssembly
from brainscore_core.supported_data_standards.brainio.stimuli import StimulusSet
from brainscore_core... |
ca80f8bc0fcabfa1403175f76a2541f56a74727f0fd2c0666816943b2b8cd09f | Python | 13,748 | 310 | import argparse
import torch
import torch.utils.data
from motion.dataset import MotionDataset
from n_body_system.model import GNN, Baseline, Linear, EGNN_vel, Linear_dynamics, RF_vel, GMN
import os
from torch import nn, optim
import json
import random
import numpy as np
parser = argparse.ArgumentParser(description='G... |
316932c6e0865c50d7178ea38bd5785ca2856c4d60dcfcc7bd035d1566cbd08a | Python | 13,751 | 467 | # Copyright (c) DP Technology.
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import contextlib
import importlib
import logging
import os
import sys
from copy import deepcopy
from functools... |
6af070478dc49668fed8bee2596d553cbe69d47a0b786566d0c30666525e74d1 | Python | 13,757 | 404 | # train.py
import pandas as pd
import warnings
import numpy as np
import scipy.sparse as sp
import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
import dgl.nn as dglnn
import h5py
import random
import os
import matplotlib.pyplot as plt
from sklearn.manifold import TSNE
from utils import (
... |
a3a31442ded4b3472764b1fc56a2737223aca3da386ef70c49486276d3214607 | Python | 13,760 | 357 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 5 18:31:24 2017
@author: ajaver
"""
import numpy as np
import pandas as pd
import tables
import warnings
from scipy.interpolate import interp1d
from tierpsy.features.tierpsy_features import SmoothedWorm
from tierpsy.features.tierpsy_features.food ... |
730842549aafba05baa6d6ce9485bce64832952686f5ef9a84f3c3b81c86860e | Python | 13,763 | 363 | # Copyright (C) 2025 Paolo Vincenzo Fioretti, Michela Roccuzzo, Enrico Saccon,
# Maria Pennuto, Manuela Basso
# 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... |
bbcd729e9f60d3bc8663ce9fb07d6f15bb9d2720ad7da68b5f5a39f78bebb691 | Python | 13,774 | 388 | import numpy as np
from nems.distributions import Normal
class Parameter:
"""Stores and manages updates to values for one parameter of one Layer."""
def __init__(self, name, shape=(), prior=None, bounds=None,
default_bounds='infinite', zero_to_epsilon=False,
initial_value='... |
97899393443e7b6fa5757c3cb3003424b6b5e2f58bd606025beb3102bb4a3077 | Python | 13,780 | 383 | from pathlib import Path
import pandas as pd
from tqdm import tqdm
from transformers import RobertaTokenizer, RobertaModel
import torch
import numpy as np
import os
from torch_geometric.data import Data, HeteroData
def get_data_dir(server_id):
if server_id == "206":
return Path("/new_temp/fsb/Twibot22-base... |
685943b32791871feb3fd75876b5895656242f32206a81f5b662620cb66744c6 | Python | 13,781 | 361 | import os
import argparse
import sys
from pathlib import Path
import numpy as np
import pyvista as pv
from PIL import Image
REPO_ROOT = Path(__file__).resolve().parents[4]
if str(REPO_ROOT) not in sys.path:
sys.path.insert(0, str(REPO_ROOT))
from cvdproc.utils.python.visualization.surface_plotting_utils import (... |
246ee9b59bf640b91aff9d43cabc49306048485c2c5cfdfa5128c7741b4b739e | Python | 13,782 | 240 | """
(C) Copyright 2019 IBM Corp.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
... |
b6bf553d14f77a352b833612aa07a598a82044cf0bf48f3777dfc985f77b03d6 | Python | 13,783 | 383 | import numpy as np
from physical_objects import Isolated, Stick, Hinge, Complex
from tqdm import tqdm
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import warnings
warnings.filterwarnings("ignore")
class System:
def __init__(self, n_isolated, n_stick, n_hinge, n_complex=0, complex_sizes=... |
3a5ec1e8939f58e1ccda5c6a79f579fc34207d8db806e3d8ea365d92c42b931f | Python | 13,785 | 312 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import contextlib
from functools import partial
from pathlib import Path
import numpy as np
import torch
from ultralytics.nn.modules import Detect, Pose, Pose26
from ultralytics.utils import ARM64, AUTOINSTALL, LI... |
a237f5e723dcac72a5cf7d940f5344777ea2b1fc33f545d73c1982ee9bd0e452 | Python | 13,786 | 440 | import celldetection as cd
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import torch
import tqdm
from torch.cuda.amp import GradScaler, autocast
from . import names
def compute_precision(true_positives, false_positives):
tp = true_positives
fp = false_positives
try:
re... |
f0e92eff20b8dbfb4b8eedc574d26154c6df3da7f11a4ef3330d560b395875bf | Python | 13,786 | 281 | #!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
import sys
import matplotlib.pyplot as plt
import matplotlib
matplotlib.u... |
660d1b97ea52cbafc8aa34f4a6a9013e98e425233a0f2b97d182aff56311a4d0 | Python | 13,789 | 389 | import os
from pathlib import Path
import pickle
import numpy as np
import nibabel as nib
from scipy import ndimage
import psutil
from joblib import Parallel, delayed
from scipy.ndimage.morphology import binary_dilation, binary_erosion, binary_closing
from sklearn.metrics import confusion_matrix
def keep_largest_bl... |
cd0b9bdd8cfdbb52e844b848c74e32a373c427ca280f1dcfb12150fc99296f72 | Python | 13,799 | 417 | from collections.abc import Callable, Sequence
from dataclasses import dataclass
from difflib import get_close_matches
from typing import (
TYPE_CHECKING,
Any,
Literal,
)
import torch
from torch import nn
from torch.utils.data._utils.collate import default_collate
from eir.data_load.data_preparation_modul... |
590ed459e04515cc4e048f542333c09291bdf3fb0608e2206d231c1d64a1f103 | Python | 13,802 | 324 | import sys
import importlib
import argparse
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset
import pyro
from pyro.infer.autoguide import AutoDiagonalNormal, AutoNormal
from tqdm import tqdm
import numpy as np
import pandas a... |
99bc22a15aa43332ccb94f274420d1b59d77ca4a741cdfc4633c7e5049e05957 | Python | 13,802 | 360 | """
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... |
e52c6a7680b4bbb84288a620d468c266ffe13bf7a37f290757bfd95ca9e1f995 | Python | 13,802 | 363 | import math
import torch
import torch.nn as nn
import torch.distributions as D
import torch.nn.functional as F
# Define two globals
bce_fn = nn.BCELoss(reduction='none')
mse_fn = nn.MSELoss(reduction='none')
Tensor = torch.cuda.FloatTensor
def add_coords(x, just_coords=False):
'''
This just the Uber CoordCo... |
971f3a856a146ed1cbdb86cb8de282540865d9d2e27c8c5b988225ef23dc7e7e | Python | 13,804 | 323 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Manuel Heger, Henrik Zunker
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance... |
8ec980e1cd686452c6ebfd7a78fe429b609df68d8ba9c0e5d8e30861a99e9303 | Python | 13,805 | 403 | """ Skill inference task.
The current version is updated version from the (semi-)final version.
Point of update is 'joystick position tracking' for the observer.
Previously, the observer agent vanished and could not track.
However, it would be nice to see whether physical imitation helps
... |
4deeb0af52c8fbaf3edda4a7569728d7c898b4e796ff42658870a1842da04a6d | Python | 13,809 | 277 | import numpy as np
def concatenate_all_trial_type_within_region(data, cell_index, start_time, end_time, fs_image):
"""
concatenate the neural activity of active cells across trials
Parameter:
- data: list of ndarray
List of neural activity arrays for each trial type. Each array... |
5fb6f4ded62a35fbeaee2689491a03da966c5ae2bd7ff7d81cef04b22c2ed9c7 | Python | 13,810 | 277 | import numpy as np
def concatenate_all_trial_type_within_region(data, cell_index, start_time, end_time, fs_image):
"""
concatenate the neural activity of active cells across trials
Parameter:
- data: list of ndarray
List of neural activity arrays for each trial type. Each array... |
eb0e62ca7eacfbf3a290a54897d09a4f75143afc8a2da4cec1cee8a4c1894f88 | Python | 13,812 | 279 | from typing import Optional, List, Dict, Union, Callable
import tensorflow as tf
from tensorflow.keras.layers import Activation
import numpy as np
from .generic import TransformerLayer, MeshLayer, CompoundTransformerLayer, PermutationLayer
from ..meshmodel import RectangularMeshModel, TriangularMeshModel, PermutingRe... |
3fedcc19115014b133f06f25159955ebfb7f092a343f4e5ba88d3fab7d0ef513 | Python | 13,815 | 385 | from __future__ import annotations
import ast
import io
import os
import re
from ast import literal_eval
import pandas as pd
import requests
import streamlit as st
import tabulate
import unicodedata
def create_article_handle(row):
author_snippet = row['author'].replace(",", "").split(" ")
if len(author_snip... |
93229b4b841373d3817eaa4f286e8aecaeab6cc4ecbe7a261ee15fdcaf7e976e | Python | 13,816 | 357 | import argparse
import networkx as nx
import matplotlib.pyplot as plt
import random
import numpy as np
import math
from scipy import stats
'''
first version: unweighted, undirected network
use edge random walk to generate edge transction matrix based on EM algorithm
'''
def parse_args():
'''
Parses the node... |
1b3671c43d02bb898c9b30e91b8c66fe41bc232d1eb9a6c58eb29669601f0df0 | Python | 13,819 | 317 | """Precursor candidate retrieval.
Every test here corresponds to a measured defect in the 3-decimal exact-bucket filter
that shipped up to 1.1.1, or to a property of the ppm window that replaced it. These
need only numpy/pandas/rdkit -- no torch, no models, no 520k-row reference database --
so they run in seconds and ... |
54ba71cb03624f479987cdfda402e474686a5690873b770062504f48ca82dd80 | Python | 13,822 | 295 | """
PyVISAScope provides an interface to different scopes.
Copyright (C) 2016 Ye-Sheng Kuo <yesheng.kuo@gmail.com>
Copyright (C) 2019 Julius Zimmermann <julius.zimmermann@uni-rostock.de>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public... |
90522a76302437f8585a51c3606daeeb6622a0e7c236fcf933e3901c0ef408e1 | Python | 13,828 | 284 | #!/usr/bin/env python
# author: Jannes Spangenberg
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
import sys
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use('Agg')
from os.path import splitext, j... |
8e52273591f467ce3c3f34a8848cd8b821412ae2c155be3929351f5c06c27f94 | Python | 13,833 | 337 | import pandas as pd
import numpy as np
import sklearn.model_selection
import matplotlib.pyplot as plt
from sklearn.manifold import TSNE
from sklearn.metrics import f1_score
import h5py
import pyarrow as pa
import pyarrow.parquet as pq
from xarray import DataArray
import math
from pandas_plink import read_plink1_bin, wr... |
a51a4716ac379ebe3bdeb87c9dbdeaef13c9c00d815aa3a17175a824f02a5f7b | Python | 13,833 | 397 | import os
# ---------------------------------------------------------------------
# IMPORTANT: Set env vars BEFORE importing fury/vtk.
# This increases the chance that offscreen rendering works in subprocs.
# ---------------------------------------------------------------------
os.environ.setdefault("LIBGL_ALWAYS_SOFT... |
48a9ac7be54d1ec9124df52c079f8101b46f9c0602c081e41aa7bc002c3abee9 | Python | 13,840 | 399 | """MagicSignature objects are an extension to inspect.Signature objects.
The basic idea is that there is a tight connection between an individual Parameter
in a function signature and an individual magicgui.Widget, and a connection between
a full function Signature (a collection of parameters) and a magicgui.Container... |
50bf75952aa223ee4f7f0c7205b71c444b69bbbcf6c08038d7149891ac05fce6 | Python | 13,841 | 357 | """Read the recording list spreadsheet, mirroring ``pipelineReadCSV.m``."""
from __future__ import annotations
import re
from dataclasses import dataclass
from pathlib import Path
import numpy as np
import pandas as pd
#: The columns ``read_recording_csv`` expects, in order. Only the position
#: matters to the rea... |
e2e7ec0ce54bf36d5903cb2c74b88b24434c7b4ed912cb899b4809112fec0aaa | Python | 13,844 | 537 | # -*- coding: utf-8 -*-
# python standard library inputs
import os
import sys
from pathlib import Path
# external inputs
import numpy as np
import nibabel as nb
from nibabel.freesurfer.mghformat import MGHHeader
from nibabel.freesurfer.io import write_geometry, read_geometry, read_label, \
read_morph_data, write_... |
844c624b1d002d0e1443a05fecc7f6afb9f9a9597786941c6faecefcca6fb16e | Python | 13,846 | 308 | import torch
import torch.nn.functional as F
import numpy as np
from torch import nn
from .utils import gaussian_kernel, circular_kernel, gabor_kernel
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
EPSILON = 1e-4
class Identity(nn.Module):
def forward(self, x: torch.Tensor, *a... |
4832614744f9f80516897e2347d0950f6018203b9cd79b9f486a1257c81257ba | Python | 13,849 | 303 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import copy
import torch
from torch import nn
from .blocks import RoPEAttention
class MemoryAttentionLayer(nn.Module):
"""Implements a memory attention layer with self-attention and cross-attention mechanism... |
fd0ae75b2fbc567b6db852bd2445fae42722745c648bef1263edc473677f3425 | Python | 13,851 | 440 | import argparse
import math
import random
import sys
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision import transforms
from compressai.datasets import ImageFolder
from compressai.zoo import models
from pytorch_msssim import ms_ssim... |
566d5347caa453b8b745eb847eb972a6467a96ffcc5c13bd9c892a4d85f92ec1 | Python | 13,852 | 236 | from __future__ import print_function
import numpy as np
import pandas as pd
import argparse
import sys
import itertools
def get_segment_range(bin_start, bin_end):
return range(int(bin_start), int(bin_end)+1)
def get_1D_peak(segment_range, MACS2_peak_ranges_list):
for segment in segment_range:
if segm... |
159788206f5a5e2704c8426963b6c392e04a519a3a67b233d3ff8c6d630d0a9b | Python | 13,854 | 385 | import os
from time import time
import torch
from torch import nn
from .protein_constants import *
from .rigid_utils import Rigid, Rotation, calc_rot_tsl
def calc_angls_prot(coords, seq, psi_angle_atoms=psi_angle_atoms, chi_angles_atoms=chi_angles_atoms):
""" note: the first three pos in dim2 is invalid """
... |
8bbdc16ed8182013bb15a1b2d797c0650249759eaefe062689e28bdc03f54b49 | Python | 13,856 | 391 | """
Adapted from: https://github.com/runopti/stg
Original authors: Yutaro Yamada https://github.com/runopti
License: MIT
Summary:
This module implements the Stochastic Gates (STG) regression framework for feature selection in neural networks.
The code was adapted from the Run Opti 'stg' repository, with mod... |
22f4ef4012ae0b12a0260155643acf69a08ca0ef1a19101ddd0ed8901fa3bec4 | Python | 13,859 | 318 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
from typing import Any
import numpy as np
import torch
import torch.nn.functional as F
from ultralytics.models.yolo.detect import DetectionValidator
from ultralytics.utils import LOGGER, o... |
b130ecc32f763121e1ffb510629071c3b14f44ab0c3248122ce0dc80ff8354df | Python | 13,862 | 327 | """
Implementation of Song et al (2020) Blind Source Separation with robust Principal Component Analysis for
Myelin Water Imaging from T2* Multi-Echo Gradient-Recalled Echo Data.
Written by Vladimir Grouza 2022
Quantitative Microstructure Imaging Lab
McConnell Brain Imaging Centre, Montreal Neurological Institute an... |
691f71956d80ca38ee558dc20b89e01acc879dc80a91bae8195e3fb6c77db45c | Python | 13,863 | 413 | """Ring-like AnalogSignal/PositionArray
subsample, simplify, interpolation, smoothing, asarray, downsample, ... all have
to be handled in a special way when we have a ring-like environment.
"""
import copy
import numpy as np
from scipy import interpolate
from collections import namedtuple
from ..core import _analogs... |
f452d85f1c20da5a9f70624791f0004313d71d584d1881f6ac68929a12eeb35f | Python | 13,863 | 234 |
import pygame
import time
import re
import numpy as np
###############
# mri
###############
def mri_scanning(screen_width, screen_height, window, stimuli_width, stimuli_height, give_a_fixed_time_interval,
entry, application_path, time_sleep, making_a_session, from_xy_to_position, from_position_to_xy... |
38d6090ae6f09f05f02c9a62400a37c8e42fff8d3f811f4c4fb3898f0674bd0a | Python | 13,864 | 372 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Henrik Zunker
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... |
f10549bf98ff112f1f7c179aab1ad2f60029da6e1bb1027c7f7f04c32d05318e | Python | 13,864 | 341 | """Test CAT-NAP's node-cartography barrier and its use of the shared 4A figures.
Run from the repo root::
uv run python python/test_catnap_cartography.py
Two things are checked here.
**The barrier.** Node-cartography roles depend on five boundaries in the
participation-coefficient / within-module-z-score plane.... |
640c40e039ddf58d7c72875f3cab241cd145509f6c5da44ddb3d1e26a51e51ec | Python | 13,865 | 426 | """This module is adapted from https://github.com/Open-Catalyst-Project/ocp/tree/master/ocpmodels/models
"""
import torch
import torch.nn as nn
from torch_scatter import scatter
from torch_geometric.nn.acts import swish
from torch_geometric.nn.inits import glorot_orthogonal
from torch_geometric.nn.models.dimenet impor... |
a05acb0cd3f984a7f71d65ac16c8dc6a6c79bcb20493c2672e3b86a63ac52dd7 | Python | 13,867 | 349 | r"""This class defines the abstraction for a backend-agnostic graph store. The
goal of the graph store is to abstract away all graph edge index memory
management so that varying implementations can allow for independent scale-out.
This particular graph store abstraction makes a few key assumptions:
* The edge indices ... |
6b9c216425e2959f1813259d97504c36961f0c578c8180a19ff4ab75d2aa75da | Python | 13,869 | 408 | #!/usr/bin/env python3
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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.apac... |
66d3c5f8fec4cfaeefe99081a6a87196cf07ce1249b2c109f98ec0c9ff477dff | Python | 13,871 | 243 | #!/usr/bin/env python3
"""Validate public-release metadata, licenses and the exact output allowlist."""
from __future__ import annotations
import json
import fnmatch
import hashlib
import re
from pathlib import Path
import tomli
import yaml
HERE = Path(__file__).resolve()
ROOT = HERE.parents[1] if HERE.parent.name... |
964a864df3ca542cf8136e60da084e90de493e494e1104b0757527dc3b48fcd0 | Python | 13,872 | 403 | import os
import time
import shutil
import numpy as np
import pandas as pd
from tqdm import tqdm
from scipy.stats import chi2
import heig.input.dataset as ds
from heig.wgs.gwas import DoGWAS
from heig.wgs.null import fit_null_model
from heig.wgs.relatedness import LOCOpreds
from heig.wgs.utils import read_genotype_data... |
d5bad7200eabba5c29894916f9cc5fee49e834ab47239d9e80d08a33c43b5ab3 | Python | 13,881 | 403 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.preprocessing import OneHotEncoder
from scipy.stats import mannwhitneyu
import torch.nn.functional as F
import torch
from .ism import SeqMatrix, MutGenerator
from . import plot_utils
from . import data_utils
class Motif(... |
0c1d2314c54cc7f322035ac442009b4bcbb75127933020a6e86e33f46c3ce458 | Python | 13,885 | 417 | # These functions were adapted from `deepreg/model/kernel.py` in the 'DeepReg' repository
# on GitHub. The original implementation can be found at:
# https://github.com/flavell-lab/DeepReg/deepreg/loss
# The code is used under the MIT License.
from typing import Tuple
import numpy as np
import tensorflow as tf
import b... |
06cd6227f8c1e8fc6640803bbf3dc7b8f08311e4392f97d4f6153886ec45e8b9 | Python | 13,886 | 283 | #!/usr/bin/python
#-----------------------------------------------------------------------
# File : patred.py
# Contents: pattern set reduction functions
# Author : Christian Borgelt
# History : 2013.01.11 file created from dectred.py
# 2013.01.12 flag setting simplified, redfn0 added
# 2013.01.... |
041668950e1836835424b3886ce26a7f6ca727811bc8b7d92433939c95171673 | Python | 13,893 | 286 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import json
from typing import Any
import cv2
import numpy as np
from ultralytics.solutions.solutions import BaseSolution, SolutionAnnotator, SolutionResults
from ultralytics.utils import LOGGER
from ultralytics.u... |
bd090a7aaf2c6d8009edbc5941b6ab96bf4962dfdc568e9da6a839543b3bff38 | Python | 13,895 | 357 | import torch
import math
import numpy as np
import PIL
import PIL.Image
import os
import json
import h5py
import time
from glob import glob
from matplotlib import pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import scipy.constants as sc
import scipy.ndimage as snd
import scipy.interp... |
29201fb3ef72dc0754b02c5bde9f69ea6a6f9a5d079779d1ae56ac0e126ac677 | Python | 13,898 | 419 | # coding=utf-8
# Copyright 2018 The Google AI Language Team 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 ... |
f8da7846ac024479d34ba8624f0afa832e50f651e1191d336b4ed38796b911ee | Python | 13,898 | 287 | import numpy as np
from sklearn.base import BaseEstimator, MetaEstimatorMixin, clone
from sklearn.utils.multiclass import type_of_target
from sklearn.linear_model import LassoCV, LogisticRegressionCV
from ..utils.general_tools import column_name_type_safe_join
# Find internal implementations
try: # Version 0.20 - 0.21... |
8b1caf086bf4d6639f2b2e22903e1a644a1fce48349934b7f3fac5e7169b94de | Python | 13,902 | 312 | import argparse
import torch
import torch.utils.data
from md17.dataset import MD17Dataset
from n_body_system.model import GNN, Baseline, Linear, EGNN_vel, Linear_dynamics, RF_vel, GMN
import os
from torch import nn, optim
import json
import random
import numpy as np
parser = argparse.ArgumentParser(description='Graph... |
960c5e618c43630d4ee12a1a4d7ceed63de0fe424a7a848bef15263f20b97c1b | Python | 13,911 | 331 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Agatha Schmidt, Henrik Zunker
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complian... |
97848e912ac4e494c79ef552a643feb5b9781edb18d81173dc97bb2ed47e62e1 | Python | 13,912 | 489 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
from abc import ABC, abstractmethod
import json
import inspect
import tempfile
import fnmatch
import multiprocessing.pool as mpp
import datetime
import sys
from itertools import repeat
from glob import glob
import warnings
import pandas as pd
import numpy as np... |
a568d1683013cc68e7d0a31ddf9bc72449caeca861fe8fe78d7e54b5040c082c | Python | 13,913 | 312 | from typing import Optional, Union
import numpy as np
from scipy.spatial import Delaunay
from scipy.spatial.distance import pdist
from scipy.sparse import csr_matrix
from scipy.sparse.csgraph import connected_components
from matplotlib import pyplot as plt
from matplotlib.collections import LineCollection,PolyCollectio... |
281804c28b3bb706daff503f12da25bc69f41814fc37554fd6f1440b61f63ac4 | Python | 13,914 | 359 | """
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... |
a9c2c546b6e160954333464ff6465fb5e04aed3578189ec60066e963d15b1ecd | Python | 13,919 | 364 | #!/usr/bin/env python3
# general imports
import numpy as np
import sys
import matplotlib.pyplot as plt
from tqdm import tqdm
import time
# torch imports
import torch
import torch.nn as nn
# PyTorch TensorBoard support
from torch.utils.tensorboard import SummaryWriter
from datetime import datetime
# utils imports
fr... |
0a7e0364bf86d8b49c915eb3ebd39708e4374bde7b28507930519b338557291a | Python | 13,922 | 457 | # 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, ... |
4c3d974ce64d9c0e36d809881d011998b9aaa8b947cce260d2a00b666f441620 | Python | 13,922 | 324 | """
Methods for Cramer-Rao lower bounds optmization of b-value schemes.
"""
import numpy as np
import numpy.typing as npt
from scipy.optimize import minimize, Bounds, curve_fit
from ivim.models import sIVIM, diffusive, ballistic, intermediate, sIVIM_jacobian, diffusive_jacobian, ballistic_jacobian, intermediate_jacobi... |
dda99c1a4efef08199235545d0834899a66e55508214749f5cd0298b2824061e | Python | 13,924 | 331 | import pandas as pd
import numpy as np
from natsort import natsorted
import cv2
from sklearn.preprocessing import minmax_scale
from matplotlib import path
from typing import List, Union, Generator
from pathlib import Path
from napari.utils.notifications import show_info
from napari_dmc_brainmap.results.results_helpers.... |
d29c422ee7b88aaa850be939072a807b28369a882d597aa0b6877764e10cab50 | Python | 13,933 | 385 | import inspect
import os
import sys
import typing
import warnings
from typing import Any, Dict, List, Optional, Set, Tuple, Union
import numpy as np
import torch
from torch import Tensor
WITH_PT20 = int(torch.__version__.split('.')[0]) >= 2
WITH_PT21 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 1
WITH_PT22... |
c8970eb7d7a49c9d97e2772c4d65f6870616f961adbde0ddc02f44f97f5bbb25 | Python | 13,934 | 369 | """
Fused Attention
===============
This is a Triton implementation of the Flash Attention v2 algorithm from Tri Dao (https://tridao.me/publications/flash2/flash2.pdf)
Extra Credits:
- Original flash attention paper (https://arxiv.org/abs/2205.14135)
- Rabe and Staats (https://arxiv.org/pdf/2112.05682v2.pdf)
- Adam P... |
9ab41423bee401fd0bfa84249f22bc0fcdcc05b9c01b3882b66424099907cfbd | Python | 13,937 | 386 | import os
import shutil
import numpy as np
import pandas as pd
import hail as hl
import heig.input.dataset as ds
from heig.wgs.relatedness import LOCOpreds
from heig.wgs.null import NullModel
from heig.wgs.coding import Coding
from heig.wgs.slidingwindow import GeneralAnnotation
from heig.wgs.mt import SparseGenotype
f... |
c8d7779adc7c2963144a2bade1e91256b08d89e818488196bb944ff3dadbabed | Python | 13,939 | 331 | import os, re
import pandas as pd
import random
import numpy as np
import nrrd
def get_all_filenames(folder_path):
filenames = []
for filename in os.listdir(folder_path):
full_path = os.path.join(folder_path, filename)
if os.path.isfile(full_path):
filenames.append(filename)
re... |
c5105d7df5be95113e714f0f551aad18e3e9d420bd91a9abdce32f79b48da339 | Python | 13,942 | 395 |
###############################################################################
#################### Boilerplate ########################
###############################################################################
import pandas as pd
import matplotlib.pyplot as plt
import os
import matplotl... |
0d4ee6930ccd375b34152bfe1d1d42f4f9ad706d2a7b4c48fbcfb5693f3e1b32 | Python | 13,944 | 431 | from typing import Any, Dict, List, Optional, Tuple, Union
import numpy as np
import pandas as pd # type: ignore
import scanpy as sc # type: ignore
from anndata import AnnData # type: ignore
from numpy.typing import NDArray
from scipy.sparse import issparse # type: ignore
from ..logger import logger
DESIGN_KEY =... |
2815ea0c6747f94ef03cd4cbbdd50e1e642f93f55f1f054f17c90f0fd1e2d5f8 | Python | 13,944 | 289 | import torch
import pandas as pd
import os
import sys
import lightning.pytorch as pl
from scipy.stats import pearsonr
from datasets import GTExDataset,GTExRefDataset
from torch.utils.data import DataLoader
from scipy.ndimage import gaussian_filter
import numpy as np
from eval_enformer_gtex import get_enformer_output_di... |
f02b8c9b62c64b34ae649b361b987b9323b03a33ac43264f63db86f273bbed41 | Python | 13,944 | 356 | # Basic imports
import numpy as np
import pandas as pd
import tqdm
import os
import glob
import datetime
# Image processing tools
import skimage.io
from skimage import (color, feature, filters, measure, morphology, segmentation, util)
import skimage.feature
import skimage.filters
import skimage.filters.rank
from ski... |
2af00c778b2b57f7e7dc5cc83d83c2fe1de4d81a733896294f94a53262815687 | Python | 13,945 | 391 | """
Doing motion correction and registering multiple runs across sessions.
"""
import ants
import os
import glob
import nibabel as nb
import numpy as np
import subprocess
import sys
sys.path.append(f'./code/misc')
from computeT1w import *
subs = ['sub-12', 'sub-15', 'sub-16', 'sub-17', 'sub-18']
# subs = ['sub-07'... |
93259dd5a81f10673d5accc9b95c5749b982d81b24ae0e2117cfdbe97769bb9e | Python | 13,947 | 348 | """How far a run has got, and how much longer it has left.
A run is a few minutes to a few hours of near-silent work, and the status log
answers "is it alive?" without answering "should I go to lunch?". This turns the
same work into a fraction and an estimate.
**Why weights, and where they come from.** Counting recor... |
b9ad933d00cfc62686ac3531b247edb1e92f0e6d37d1eb771ce564ebf52b7716 | Python | 13,947 | 334 | import jax
import jax.numpy as jnp
import matplotlib.pyplot as plt
import glob
import sys
import os
import re
import json
from scipy.linalg import toeplitz
plt.rcParams["font.sans-serif"] = ["DejaVu Sans"] # Best available
plt.rcParams["font.family"] = "sans-serif"
plt.rcParams.update({
"font.size": 10,
... |
62d7d4e83549ebd0248faf9d5f871b1e449b02f93722b9ecc41e47b0f56b80a9 | Python | 13,948 | 380 | # 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, ... |
25966e843a332aa06fa622c64c0f6f032a19c9edb2b8952f968293c33330d61b | Python | 13,950 | 373 | """Collection of functions to evaluate brain sensitivity selectivity and crossing ToFs
"""
from dataclasses import dataclass
from typing import Optional
import numpy as np
from scipy.ndimage import gaussian_filter1d
from scipy.signal import find_peaks
@dataclass
class Metric:
corr_per_pulse_brain: np.ndarray
... |
de790cbfbeed1c72903af4d296056c246e7420f3045a2fe4262eb4c7b939ab36 | Python | 13,951 | 370 | import sys
import yaml
import os
import numpy as np
import re
import matplotlib.pyplot as plt
from scipy import stats
import h5py
pathpath,myrun,ncluststr,cmethod,get_rois_bool_str,roi_tag = sys.argv[1:]
'''
pathpath = 'PATHS/filepaths_carlen.yml'
myrun = 'runCrespZP_brain'
get_rois_bool_str = '1'
cmethod = 'ward'
n... |
31fb94612b080c55b5d02c65985e3016b0e7f53535c9a1c5cad53eb59c6371af | Python | 13,953 | 364 | import os
import shutil
import subprocess
import tempfile
import warnings
from abc import ABC, abstractmethod
from collections import Counter
from datetime import datetime
from pathlib import Path
from typing import List, Optional, Union
from loguru import logger
from brainles_preprocessing.brain_extraction.brain_ext... |
503edb397ac6b414e0cff915761c81ecd8d4541b28d34b7c424edb02b0c20918 | Python | 13,959 | 407 | # -*- coding: utf-8 -*-
"""
File to get Fig. S17 (section 4)
"""
import scanpy as sc
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import matplotlib as mpl
import os
import warnings; warnings.simplefilter('ignore')
import anndata
from scipy.stats import p... |
37668e5c11102110ac48592f6df52613148db70a9ceec323c49a7963cbd20268 | Python | 13,964 | 413 | from collections import OrderedDict
from torch import nn
import math
import torch.nn.functional as F
import torch
import numpy as np
from timm.models.registry import register_model
HASH = '5c427c9c'
HASH = '1d3f7974'
class Flatten(nn.Module):
"""
Helper module for flattening input tensor to 1-D for the use... |
48ff4606a10c8e3b6deade640242efcea63cff3760540daebd33d8616f8a9692 | Python | 13,966 | 377 | from pathlib import Path
import numpy as np
import polars as pl
from polars.exceptions import SchemaFieldNotFoundError
from typing import Literal, Any
from neuralib.util.verbose import fprint, print_save
from rscvp.util.cli import CodeAlias, HEADER, CELLULAR_IO, CommonOptions
from rscvp.util.cli.cli_statistic import ... |
4f2082ab52cccce5952bdea2948daa9247e71cf8d23366aee935967c7913a705 | Python | 13,984 | 407 | import logging
import random
from collections import defaultdict
from collections.abc import Callable, Generator, Sequence
from dataclasses import dataclass
from pathlib import Path
from typing import (
TYPE_CHECKING,
Any,
)
import numpy as np
import pandas as pd
import seaborn as sns
import torch
from captum.... |
74db09347d12f9acbb92b2cae71d81be3bb09761730f1fabf6242f9da9b59c20 | Python | 13,984 | 440 | # utils.py
import os
import torch
from monai.transforms import (
LoadImaged,
EnsureChannelFirstd,
Orientationd,
Spacingd,
ScaleIntensityRanged,
EnsureTyped,
RandCropByPosNegLabeld,
CastToTypeD,
ToTensord,
Compose,
NormalizeIntensityd,
CenterSpatialCropd,
RandFlipd,
... |
cda54e10bba0e3993faac65d573b3ef6c2cb11b3803f294b1073495d3be47452 | Python | 13,986 | 418 | from __future__ import annotations
from datetime import datetime, timezone
from pathlib import Path
from typing import TYPE_CHECKING, NamedTuple
import numpy as np
import pandas as pd
from tqdm import tqdm
import seisbench
from seisbench.data.base import WaveformDataset
try:
from pyrocko.gui.marker import Phase... |
972452f11ea26c16906247be8c14e30f669f0fcf72a0a1d889d76277e34d7e75 | Python | 13,989 | 375 | import numpy as np
from random import shuffle
from .data_utils import DataGenerator, _revcomp
class SeqMatrix():
'''Parent class for inheriting. Used for making insertions/substitutions \
dynamically '''
pass
'''class RandomSeq(SeqMatrix):
def __init__(self, p, length):
self.p = p
... |
23a9ffc43f23a5784e61c002f0fa9606962030281fc0803802e437c9317e891f | Python | 13,992 | 386 | """`guiclass` decorator.
1. Turns a class into a dataclass
2. Uses `psygnal.evented` to make it an [evented
dataclass](https://psygnal.readthedocs.io/en/latest/dataclasses/)
2. Adds a `gui` property to the class that will return a `magicgui` widget, bound to
the values of the dataclass instance.
"""
from __future_... |
197c9eff43d607b696303c47c11dbb0d7ad172416a949cc499198a140c4f3b03 | Python | 13,993 | 359 | # 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, ... |
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