sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bea4e8e0a089e61a4ca98d9c8e408544e09b84a14afccb5b80661176722ed168 | Python | 12,122 | 329 | #
# 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,... |
d6bee1dbf1ac03f43816404c6e43952414fcd038bd666f512453eb6cbe36ab58 | Python | 12,123 | 292 | """"""
"""
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... |
1f83a12c6a73991fb8dd535cf2f5f51192ac7019d6f3d0f70b76b4bdf4bf10af | Python | 12,125 | 386 | # 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... |
0d5136d783344e6f2178f390eb5090bf67bc856a19e85f6dd5abaafcf9c1856f | Python | 12,128 | 281 | #!/usr/bin/python3
import os
import argparse
import numpy as np
import tensorflow as tf
from tensorflow.python.keras.callbacks import TensorBoard, ModelCheckpoint, \
EarlyStopping
# imports from this package
import utils
from cnn_lib import AugmentGenerator
from architectures import create_model
from visualiza... |
91ed109b7aaf7fb4eb708e1ef8c923b7390a36006921742bcc541b152c9f3071 | Python | 12,128 | 220 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
# Function to read several connectomes and generate from these a ConnectivityMatrix object using conntility
# The code is taken from:
# https://github.com/BlueBrain/ConnectomeUtilities/blob/main/examples
import con... |
8f92848b93bf550e464b9f47e3d97ed7483350e9162b197019e54c9463b630c9 | Python | 12,130 | 362 | """
pygments.lexers
~~~~~~~~~~~~~~~
Pygments lexers.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import sys
import types
import fnmatch
from os.path import basename
from pip._vendor.pygments.lexers._mapping import LEXER... |
9108c7b4c2f1bb198e8e2ffc2ab9ee198b47b053a7c6597f9b65ef37a8664285 | Python | 12,133 | 397 | # 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... |
b071e1921e8ccc4a8a072031d5dca3c8b69f4dd7ce72f3fc16bc526a728d2810 | Python | 12,134 | 382 | # 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... |
426da5f6096feb3d264a79c4812250fdda36e11ec20ee4011cdc65bd5e7e77fd | Python | 12,135 | 314 | import numpy as np
import pandas as pd
import pytest
import scanpy as sc
from anndata import AnnData
from scipy import sparse
import pertpy as pt
from pertpy._types import cast_frame
@pytest.fixture
def dummy_adata():
n_obs = 10
n_vars = 5
rng = np.random.default_rng()
X = rng.random((n_obs, n_vars))... |
b95933228bd758bf635e10e6303a27e591900a1949da02dc73c0d19f6c88cd35 | Python | 12,136 | 293 | from .LibFwdBwd import FwdBwdAlg_cpp
from scipy.special import psi
import numpy as np
# ################################################################
# Compress - Expand Methods
def log_expand(pi, tmat, states, n, k, likelihood=None, obs1=None, obs2=None):
# ###################################################... |
dcea29b2d1bcebd80ebddb70b832b7841e7cfb2955a76513deac3bc111ec8c1c | Python | 12,143 | 346 | # ------------------------------------------------------------------------
# Copyright (c) 2022 megvii-model. All Rights Reserved.
# ------------------------------------------------------------------------
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
class AvgPool2d(nn.Module)... |
5521ad0898c7ac2446ebc7f2f6bce41a3a2f873fe37f7dec3c346735b80ad09c | Python | 12,144 | 329 | #!/usr/bin/env python3
""""
-------------------------------------------------------
reproduceReentry.py Reproduce reentries in a 3D
atrial geometry with a given .par
and .roe state files. Reentries were
induced following the P... |
832042328221ee521744640a1caefc8c9cc44bab60e3d6329da0b44af9ed275f | Python | 12,149 | 253 | # set QT_API environment variable
import os
import sys
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
# app specific libraries
import control.widgets as widgets
import control.camera_toupcam as camera
import control.core as co... |
f181c4af8b26a6481ff83d550da0b5d5792602ab34f428c699a7ecd8f82db7d0 | Python | 12,149 | 408 | import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl.function as fn
from dgl.nn.pytorch import SAGEConv
"""
GraphSAGE:
William L. Hamilton, Rex Ying, Jure Leskovec, Inductive Representation Learning on Large Graphs (NeurIPS 2017)
https://cs.stanford.edu/people/jure/pubs/graphsage... |
70bb62d543f7850b01e168315a14388b860829aff06d5467186de8129309b868 | Python | 12,151 | 260 | '''
Script to track offline from python without having to load an APT project into front-end.
'''
import sys
import os
import shutil
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import argparse
from tarfile import TarFile
import tempfile
import glob
from pathlib import Path
from datetime import datetime
import APT_interf... |
cac7edf79bca502ebe3921332d890078874496bf15912991119f64ade8b1d2e8 | Python | 12,151 | 256 | import os
import pickle as pkl
from typing import Callable, Dict, Tuple, Union
import numpy as np
from ....utils import get_random_dir_path
from ..base_dataset import BaseDataset
class SEEDVFeatureDataset(BaseDataset):
r'''
The SEED-V dataset provided by the BCMI laboratory, which is led by Prof. Bao-Liang ... |
3876ddf1f719b1800418b8b3821350b9c524428b36fdd1aeafa05fa93f15677c | Python | 12,153 | 311 | import os
import logging
import json
import pickle
import numpy as np
import torch
from typing import List, Optional
from torch.utils.data import Dataset, DataLoader
from lightning.pytorch import LightningDataModule
from cellmincer.models import \
get_temporal_order_from_config, \
get_window_padding_from_co... |
9ee52e6fc294596bf85a6c7a14112d63100e0b5432073d2c1f907320e546c577 | Python | 12,153 | 384 | """
Utilities for converting Open Images format CSV datasets to/from FiftyOne
Dataset representation.
| Copyright 2017-2022, Voxel51, Inc.
| `voxel51.com <https://voxel51.com/>`_
|
"""
import glob
import os
import numpy as np
import pandas as pd
import fiftyone.core.dataset as fod
import fiftyone.core.labels as fol
... |
362b8b6fd25b2c097233c7f9277cf9bdb4974560f4acb3c4a0e23c44812f9676 | Python | 12,156 | 256 | # coding=utf-8
# Copyright 2018 The Open AI Team Authors and The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... |
251e02ef74b9a382ecfd861a6a5c217db5abf8dca5c8f0eb4f21e80eb256550c | Python | 12,158 | 286 | #! /usr/bin/env python
# ==============================================================================
# Copyright (c) 2021, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Re... |
34fd64ffdf9138a0715a855b1625e157c496e69a80ad37a29e90a520c694a58d | Python | 12,159 | 261 | """Abstract base class for loading HED schema files into HedSchema objects."""
from abc import ABC, abstractmethod
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.schema import hed_schema_constants, hed_schema_constants as constants, schema_header_util
from hed.schema.hed_schema import HedSchem... |
4cafdc8e968e34db79a9aa954104e44a6bc6d22f1a3068c35c2df3350a4cf194 | Python | 12,161 | 291 | """
Script for comparing statistics from different profiles
Only slices which are compatible can be compared
Input: - Path to the input profiles for comparing
Output: - Plot graphs with the statistical comprison
- Store a FuncComparer object in pickle file
"""
__author__ = 'Antonio Mar... |
c1d88d49d66011b792749fbd3eb8af151996ca7b19021618a3df760f1f32bfe2 | Python | 12,167 | 415 | class UnificationFailure(Exception):
pass
class Occurs(UnificationFailure):
pass
ARROW = "->"
class Type(object):
def __str__(self): return self.show(True)
def __repr__(self): return str(self)
@staticmethod
def fromjson(j):
if "index" in j: return TypeVariable(j["index"])
i... |
880fa2697cd225e595fbbbf1b17f1954216f87dd9ff85f20c11ad6c83629a539 | Python | 12,168 | 334 | import os
import cv2
import time
import random
import re
import string
import numpy as np
import pandas as pd
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset
from torch.nn.utils.rnn import pad_sequence, pack_padded_sequence
import albumentations as A
from albumentations.pyt... |
55f2211cf51e7d96c19156591450c34416490a7f3e442a91a51419f0e9815fb5 | Python | 12,172 | 337 | import pickle
import bpy
import MDAnalysis as mda
import numpy as np
import pytest
from MDAnalysis.analysis.hydrogenbonds import HydrogenBondAnalysis
from nodebpy import geometry as g
import molecularnodes as mn
from molecularnodes.nodes.geometry import FindHBonds, StyleHBonds
from .constants import data_dir
pytestmar... |
c150ec3e23e716f36be5909e475ce94e0fd2bb577625db936de41b3bc281eb18 | Python | 12,172 | 305 | """
CLI stitching pipeline script.
Usage:
python -m regtools.stitching.pipeline --input_dir /path/to/tiles --output_dir /path/to/output
python -m regtools.stitching.pipeline --input_dir /path/to/tiles --output_dir /path/to/output --section 5
python -m regtools.stitching.pipeline --input_dir /path/to/... |
02ac97a40d854050fb93e6ee06dcbfee2b461189219956bc5f4f4d2d1ba5dd03 | Python | 12,176 | 261 | ######################## BEGIN LICENSE BLOCK ########################
# The Original Code is mozilla.org code.
#
# The Initial Developer of the Original Code is
# Netscape Communications Corporation.
# Portions created by the Initial Developer are Copyright (C) 1998
# the Initial Developer. All Rights Reserved.
#
# Con... |
3f4ec646d2c6c27337f56ba3c965274de3fc43220c5c7d2b3dfa2e33e7357fae | Python | 12,178 | 373 | """Implementation of CLI render command."""
import numpy as np
from treem import Morph, SWC
from treem.utils.geom import rotation
# pylint: disable=wildcard-import
# pylint: disable=unused-wildcard-import
# pylint: disable=redefined-builtin
from OpenGL.GL import *
from OpenGL.GLU import *
from OpenGL.GLUT import *
... |
7cb16323f824f41d02e0103be43d362c6cb7484e06eb24107004af216edd2c96 | Python | 12,183 | 338 | """"""
import time
import statistics
import logging
from pupil_recording_interface.decorators import device
from pupil_recording_interface.device.video import BaseVideoDevice
from pupil_recording_interface.utils import monotonic
from pupil_recording_interface.errors import DeviceNotConnected, IllegalSetting
logger = ... |
9273867a9ee808625909e9d84f9845ee1d7082e57f22e8f52a7decdba67f5373 | Python | 12,183 | 303 | from typing import TYPE_CHECKING, List, Optional, Union
import numpy as np
from ..file_utils import add_end_docstrings, is_tf_available, is_torch_available
from ..modelcard import ModelCard
from ..models.bert.tokenization_bert import BasicTokenizer
from ..tokenization_utils import PreTrainedTokenizer
from .base impor... |
d96531bc144c98d4409fb46d3fbb3bd7c1ee7108e5818f50875d498f32ff7b37 | Python | 12,183 | 295 | """Allows output of HedSchema objects as .tsv format"""
import pandas as pd
import hed.schema.schema_io.df_constants as constants
from hed.schema.hed_schema_constants import HedKey, HedSectionKey
from hed.schema.hed_schema_entry import HedTagEntry
from hed.schema.schema_io.df_util import (
create_empty_dataframes... |
cd997e78dee5693d2a8a355ecf719eaddad055525c7cf86ff4857c0b0b7fdf0c | Python | 12,184 | 322 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from core.region_loss import RegionLoss
from cfg.yolo_cfg import *
#from layers.batchnorm.bn import BN2d
class MaxPoolStride1(nn.Module):
def __init__(self):
super(MaxPoolStride1, self).__init__()
def forward(self, x... |
d28168dde88076c2ebdd6be037735b4d0b6ba1f18638b97c8199953d4f194c95 | Python | 12,185 | 281 | """EEG/MEG BIDS data format reading.
This module provides functions for reading BIDS data format
"""
import re
from copy import deepcopy
from typing import Callable, Optional
import mne_bids
import numpy as np
from mne import events_from_annotations, set_log_level
from mne.channels import DigMontage
from mne_bids.co... |
6fd66c64fe35a851c17698d2592777ed87cb28def1c6b50b5a8038ea423cc895 | Python | 12,188 | 233 | # 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... |
24b1b24d49ef5b2854c7c1bdf4b9c125318ae16a41ece8da7cf690f79f9ce729 | Python | 12,192 | 348 | # -*- coding: utf-8 -*-
"""MultimodalModel
Automatically generated by Colaboratory.
Original file is located at
https://colab.research.google.com/drive/15pdn81YOduRd53j_2K8yN4mf4RRuv5PL
# Mount the drive
"""
from google.colab import drive
drive.mount('/content/drive')
"""# Setting features"""
import pandas as... |
3bdb5a52d7e167e5b7777fdd47c4e7d1723a6319feac3b1ba4eb4a3ace1cf538 | Python | 12,194 | 312 | # %% [markdown]
# # Segmentation and Region Properties Extraction for Enteric Neurons and Macrophages
#
# **Author(s):** Piyush Amitabh
#
# **Description:**
# This script processes downsampled images to segment Enteric Neurons and macrophages, and extracts their region properties. The extracted properties are saved to ... |
acd395fc8e88e5bc47a98ec7cf71602563c64e8ac5602065bb471d1ae6c41970 | Python | 12,205 | 360 | """
Contains class Density for the calculation of densities of gray images along
segments.
# Author: Vladan Lucic (MPI for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import range
#from p... |
50fab941d8a972f10de0dadb2e9bbb5c98c4456a1423552e783d8bf6ee0344b6 | Python | 12,207 | 337 | from abc import abstractmethod
from collections import defaultdict
from pathlib import Path
import pandas as pd
import numpy as np
import torch
from copy import deepcopy
import torch.nn.functional as F
from torch import autocast
from torch.cuda.amp import GradScaler
from wsilearn.utils.cool_utils import is_dict, is_it... |
cac1d54763dbc0b2632e12b2a79c4ccba22fe599f0d11152814713a2c64af7d2 | Python | 12,207 | 132 | """BUILD_ATLAS_PAGE.py 2026-10-09. Writes REPORT/atlas_page.html: the sign atlas as one self-contained page (data embedded from
06-OUTPUT/release/SIGN_ATLAS.csv and SIGN_PROBABILITIES.csv, figures F19 and F20). Descriptive; every number is read from an output.
usage: python BUILD_ATLAS_PAGE.py"""
import os, json, ba... |
b28bee19c474ccec3a5e84e3d94b31e6d9b5a66be78cb868e6884350c35b5a39 | Python | 12,209 | 349 | import inspect
import warnings
from collections.abc import Sequence
import torch
from torch import nn
from torch.nn import functional as F
from torch_scatter import scatter_mean
from torchdrug.layers import functional
class MultiLayerPerceptron(nn.Module):
"""
Multi-layer Perceptron.
Note there is no ba... |
0d09f52a12fa63060338021fed9668ef95292b423fb8d80edea9b5d7515b077c | Python | 12,211 | 370 | import numpy as np
from sklearn.base import BaseEstimator, ClassifierMixin
from sklearn.utils.validation import check_X_y, check_array, check_is_fitted
from sklearn.utils.multiclass import unique_labels
from sklearn.metrics import euclidean_distances
from sklearn.linear_model import LogisticRegression
from sklearn.svm ... |
4814c54b34dfe401fb0b414d1fe59f3fdf68f39d9b257e23e338759be655eeaa | Python | 12,211 | 386 | """Large and simple widget to indicate settings/Settings.
"""
from logging import getLogger
from PyQt5.QtCore import QSettings, Qt
from PyQt5.QtWidgets import (QDialogButtonBox,
QDialog,
QFormLayout,
QGroupBox,
... |
313401a533659876c98c21c3075548c7ee40a052efad55c6cbbf6d643b5a91c8 | Python | 12,212 | 323 | """
General Classes for the package
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 15.09.15
"""
__author__ = 'martinez'
from pyseg.globals import *
import graph_tool.all as gt
from .variables import *
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
try:
impor... |
281d994649683e0c3edaf9a194e93568a984b11b4dddbe592f0bb08a56b67784 | Python | 12,215 | 326 | # 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... |
0f2d5b5a1932770da4f76f3961fb1d635231f6121dc471ad49d2cd806f73ef15 | Python | 12,216 | 296 | from __future__ import print_function, division
import numpy as np
import time
from collections import Counter
from pybullet_tools.utils import elapsed_time
from learn_tools.active_learner import ActiveLearner, format_x, THRESHOLD, tail_confidence
from learn_tools.learner import rescale, DEFAULT_INTERVAL, TRANSFER_W... |
aba4acd523b6c964d138dfe1887ddc870098e698ee401dfec96fa2d94676d1f9 | Python | 12,216 | 405 | import argparse
import logging
import os
import pathlib
from typing import Any
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
import tqdm
from matplotlib.axes import Axes
from sklearn import metrics
from sklearn.base import BaseEstimator
from sklearn.ensemble import RandomFor... |
b8459ca0297a9033d92105fa58cabbcb00b49f66ad06f12e83be682351f8bd4c | Python | 12,223 | 395 | """Functions for handling and inspecting data
"""
import os
import pickle
import mne
import numpy as np
import pandas as pd
from scipy import spatial
def _get_device_fids(raw, include_origin=False):
"""Get fiducials in the M/EEG device space.
Parameters
----------
raw : mne.io.Raw
An MNE... |
22aac8ecf1450bf28a0d8275b0c3bc5b8a1a3c8cebeb2ae7b42003261c1e79a3 | Python | 12,224 | 248 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
"""
Plotting oracle score (kind of reliability) against simplex dim (and position within simplex) for MICrONS
author: András Ecker, last update: 02.2024
"""
import os
import numpy as np
import pandas as pd
from sci... |
8d9edfb8a0ecf2d14c477353e9f23c4248a6d6f7f5715c7145b8338bc01a6828 | Python | 12,227 | 322 | # 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... |
7923feb3248439bc95f116cfe975a05ab6abac5c88b25cc12dfd91800e337179 | Python | 12,228 | 358 | # 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... |
01e661f5e9ec28b148e455698274d1e8ff389bbfdcccd78ee762f33d9f0db889 | Python | 12,229 | 319 | import datetime
import json
import logging
import os
import re
import sys
import urllib.parse
from pathlib import Path
from typing import Callable, List, Tuple
from urllib.parse import urlparse, unquote
import boto3
import requests
from requests.adapters import HTTPAdapter, Retry
from tqdm.contrib.concurrent import th... |
a1658de11d38889311c3a3d045475f172199a2c1feee6df70501b2be52f5b2f8 | Python | 12,230 | 290 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import cProfile
import pstats
import numpy as np
from examples.pybullet.namo.stream import BASE_LINK, get_base_joints, set_base_conf, get_custom_limits, \
get_test_cfree_conf_pose, get_test_cfree_traj_pose, get_grasp_generator, get_ik_f... |
91535137db6de885eb8431405f437e16760047b7d7f0277e2bbf36a5b2cd52f3 | Python | 12,231 | 360 | """Implementation of CLI render command."""
import numpy as np
import OpenGL.GL as GL
import OpenGL.GLU as GLU
import OpenGL.GLUT as GLUT
from PIL import Image, ImageOps
from treem import SWC, Morph
from treem.utils.geom import rotation
_HELP = """
interactive commands:
mouse left drag rotate
mouse r... |
93271a714764f275921ad5b2dd12d923c2337df94ee79c329d19373b525b7057 | Python | 12,240 | 305 | # -*- coding: utf-8 -*-
"""
Created on Aug 8 2022
@author: Jonas A. Thiele
"""
import pandas as pd
import numpy as np
from scipy.stats import kurtosis, skew
from random import randint
import matplotlib.pyplot as plt
#%% Functions
#Compute total number of subjects
def get_sample_size(families_all... |
1d945cac37d99224cad85e8f11b86a5011c879e1891f7cb373a4e44609c6e5d5 | Python | 12,242 | 277 | """ Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This is the main file provides ENSEMBLE of binary CNN and ViT models for end-to-end solution for what is mentioned in the paper.
# Update paths to processed datasets
# All libraries
if __name__ == '__main__':
import warnings
warnings.simplef... |
11a7c4e085b834d37a06079f49df2b51e1d59fa2de9dee3406961eb9326701d2 | Python | 12,248 | 309 | """
Script for extracting an analyzing a GraphMCF with a segmented membrane
Input: - A STAR file with a list of (sub-)tomograms to process:
+ Density map tomogram
+ Segmentation tomogram
- Graph input parameters
Output: - A STAR file with the (sub-)tomograms and their co... |
3aad7d091e976f9cf94043b7bc3a873806bca8fa66932c72bcb86a6beea4c5f8 | Python | 12,250 | 340 | import os
from typing import Dict, Union, List
import ase
import numpy as np
import torch
from schnetpack.transform import MatScipyNeighborList
from spainn.interface import NacCalculator
from spainn.properties import SPAINN
__all__ = ["SPaiNNulator"]
class SPaiNNulatorError(Exception):
"""
SpaiNNulator err... |
9e24dcb05aec5f3284d9052522d0a0e54ab5c8ef1bc03ce107ba175fa58b141d | Python | 12,254 | 406 | """
(*)~---------------------------------------------------------------------------
Pupil - eye tracking platform
Copyright (C) 2012-2019 Pupil Labs
Distributed under the terms of the GNU
Lesser General Public License (LGPL v3.0).
See COPYING and COPYING.LESSER for license details.
------------------------------------... |
fadb8b21f22dac902d6b12aa95467e06fae6372261a6921d151ea614dd58a2cc | Python | 12,259 | 310 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2023/7/21 14:05
# @Author : piaoyang cao
# @File : run_class.py
import argparse
import torch
from torch_geometric.loader import DataLoader
from torch.optim.lr_scheduler import StepLR
import numpy as np
import torch.optim as optim
from tqdm import tqdm
... |
ae9a1fb5c5be97a04172830942c5c8b279e34020a18b5fe34eadafac00271b17 | Python | 12,261 | 290 | # 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... |
36b3e24c1c715ed997e645955c77fd2337792c52cfa1ed85f9bdf11eea86424b | Python | 12,265 | 294 | from __future__ import print_function
import os
import numpy as np
import datetime
import random
#from ast import literal_eval
from learn_tools.collect_simulation import SKILL_COLLECTORS
from learn_tools.learner import DEFAULT_INTERVAL, rescale, sample_parameter, x_from_context_sample, SKILL, FEATURE, \
PARAMETE... |
fc377fee153b74bc4ea75a1209de1ef51e348b5b4afe532a0b9ba07572dd8d17 | Python | 12,270 | 287 | import linecache
import os
import sys
sys.path.append(os.path.dirname(__file__))
import time
import copy
import numpy as np
import csv
import apps
import arrayexp
import arrayparams
import reram_register
# ARRAY info
# POSITIVE_READ = 0
# NEGATIVE_READ = 1
class ARRAY4K:
ID = 1#SDK.ARRAY1
R... |
0f844316d0432cd511eb4356ecbe7273c0aa32d7f6730800c4b2708d4439fee1 | Python | 12,272 | 287 |
import os
import argparse
import lxml.etree as ET
import math
import carla
from utils import ALL_TOWNS, \
parse_annotations_file, interpolate_trajectory, scan_route_for_scenarios
ID_START = 0
MAX_LEN = 380
def main(args):
route_id = ID_START
road_type = args.road_type
root = ET.Element('routes... |
117866bf09fb1ea33bbe68780517ea05a4483e438a78d1e48514f1a86912b91a | Python | 12,276 | 326 | # basic
import os, math
import numpy as np
# pytorch
import torch
import torch.nn.functional as F
from torch import nn, Tensor
from torch.autograd import Variable, Function
class WaveNetModel(nn.Module):
'''
A Complete Wavenet Model
Args:
layers (Int): Number of layers in each ... |
258192dabd899f15fe79b4f3183e1f0487cded151392b42aa1cd2bd6c2d3d957 | Python | 12,277 | 327 | import os
import sys
import torch
import numpy as np
import cv2
import matplotlib.pyplot as plt
from PIL import Image
from PyQt5.QtWidgets import QApplication, QLabel, QMainWindow, QFileDialog, QVBoxLayout, QWidget, QPushButton
from PyQt5.QtGui import QImage, QPixmap, QPainter, QColor
from PyQt5.QtCore import ... |
7ff8b6868d6c5648d20886fc0409197a0fe3326b4a976bb70aeab14bdf5afadf | Python | 12,280 | 291 |
""" Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This file provides inference code for multiclass DCNN and ViT models mentioned in the paper.
# Update paths to processed datasets
if __name__ == "__main__":
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
... |
a5978d3b5bef4ab93c2dffc0ada47f339bae939377cee273963004ff7480562b | Python | 12,280 | 310 | """
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 software: yo... |
1aacbf3633a8c92ffad6eee5d12140668f95a6b6fd46772b3c84608a36c76dbb | Python | 12,281 | 263 | # -*- coding: utf-8 -*-
import torch
import torch.nn as nn
from supar.config import Config
from supar.models.dep.biaffine.model import BiaffineDependencyModel
from supar.models.dep.biaffine.transform import CoNLL
from supar.modules import MLP, Biaffine, Triaffine
from supar.structs import Dependency2oCRF, MatrixTree
f... |
f472c998c64324d24c5d9edc2f48e608c248d790ee9f33f21fb71079f68f23cd | Python | 12,281 | 290 | import abc
import copy
from typing import Optional, Tuple, Union
import numpy as np
from meep.timing_measurements import MeepTimingMeasurements
import meep as mp
from meep import binary_partition_utils as bpu
class AbstractChunkBalancer(abc.ABC):
"""Abstract chunk balancer for adaptive chunk layouts in Meep sim... |
e78eea81c68537fd0748afdd79289f4bd689385cb5ea185e6893d4f861ae89ef | Python | 12,286 | 341 | import copy
import functools
import os
import blobfile as bf
import torch as th
import torch.distributed as dist
from torch.nn.parallel.distributed import DistributedDataParallel as DDP
from torch.optim import AdamW
from . import dist_util, logger
from .fp16_util import MixedPrecisionTrainer
from .nn import update_em... |
719e2d80e50e90ae0b738dfe2284e3e301cc1ef1dba1c04130b212770ef40f8f | Python | 12,287 | 358 | # 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... |
556b4fa93fd7c84e961e8c48342b5596616c4274fb1c005a4853296e283a007f | Python | 12,292 | 346 |
import os
import numpy as np
import nvidia.dali.fn as fn
import nvidia.dali.math as math
import nvidia.dali.ops as ops
import nvidia.dali.types as types
from nvidia.dali.pipeline import Pipeline
from nvidia.dali.plugin.pytorch import DALIGenericIterator
# inspired by the NVIDIA nnU-Net GitHub repository available a... |
39e43bd1d1358e5f4538db23484de31cc6655c2c4d919ed4acac613f1ac935f2 | Python | 12,295 | 307 | import os
import shutil
import time
from datetime import datetime
import numpy as np
import torch
import torch.backends.cudnn as cudnn
from torch.autograd import Variable
from src.training.tdrg_utils import AverageMeter, AveragePrecisionMeter
class Trainer(object):
def __init__(self, model, criterion, train_loa... |
6a9b3d676bfc9348c6d6efc7f9fbbc3236486df31b227b41208823d15120d2e4 | Python | 12,295 | 260 | from warnings import filterwarnings
filterwarnings('ignore')
import os, sys, argparse
# analysis module imports
from model_opts import *
from brain_data import *
from ridge_gcv_mod import RidgeCVMod
from sklearn import preprocessing
def get_splithalf_xy(feature_map, response_data, scale = True):
data_splits = {... |
fa5e53a53b766f1bac1211a8b86d83f9a37f602c80483199235ccf41a821c20c | Python | 12,302 | 266 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 21 22:39:05 2018
@author: Carlos A Ariza, PhD
"""
#import pickle as pkl
import pandas as pd
from itertools import combinations
#import matplotlib
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import seaborn
#feat_df = pd.read... |
12a42b9359f0b46c70b2a3d22c35e38c6a763b83d3fa1f852d9952f99019758c | Python | 12,304 | 255 | #!/bin/env python3
"""
Properties of pulses
--------------------
This submodule contains tools to compute properties of the impulses
propagating across the medium.
In cardiology, these are for instance *action potential duration* (APD) and
*conduction velocity* (CV).
"""
import numpy as np
from typing import List, T... |
ca03352b41430666fabc1adcfd23615d9e7c7ad41e514e47908a4e5f3b2f841e | Python | 12,306 | 377 | import pandas as pd
import numpy as np
import os
import h5torch
import ast
import argparse
from maldi_nn.utils.metrics import *
from maldi_nn.spectrum import PeakFilter
from maldi_nn.models import AMRModel, MaldiTransformer
from lightning.pytorch import Trainer
from maldi_nn.utils.data import DRIAMSAMRDataModule
from m... |
2c6152f4f6e312f8dd14cd8704df6aaf35bb6395447361e679e79ae958b60d01 | Python | 12,309 | 252 | # Load packages
import pandas as pd
import numpy as np
from subprocess import call
import subprocess
import concurrent.futures as cf
import os
import sys
import json
import networkx as nx
from scipy.sparse import load_npz
import scipy
import pickle
from pyflagsercontain import compute_cell_count
config_address = sys.a... |
b75968f716b812d306fa4cace5f9f951c17f4c2abfb601dc6efc0e5a4505a735 | Python | 12,313 | 332 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Modular prediction of off-target effects
@author: Wei He
@E-mail: whe3@mdanderson.org
@Date: 05/31/2021
"""
#################### Import all the packages #####################
from __future__ import division
import pandas as pd
import math,json,os,pkg_r... |
8c80fe5ee1f628cc055639672fa619742e90ad37ba76b832312299905c8f2fb9 | Python | 12,314 | 343 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import h5py
import numpy as np
import os
from pathlib import Path
import matplotlib.pyplot as plt
from scipy.io import loadmat
from scipy.ndimage import uniform_filter
from scipy.interpolate import interp1d
from ... |
8b279433aa913398f9fde37137d42ba41218c2dfbbcd5eefca19b1b086a6654a | Python | 12,320 | 234 | import numpy as np
from scipy.spatial import KDTree
from scipy.sparse import csr_matrix
from .. import config as CFG
from ..utils.misc import index_traverse, mytqdm, Timer
from ..utils.mpi import is_master, comm, distrib_vec, mpi_sum_csr
from ..matao.mataocsr import MatAOCSR
t1 = Timer('OrbProd')
t2 = Timer('OrbPairT... |
2b4c723bd43b2d37f604a201c2d0b1e0d017cccef4dbdb831934bdee415d6c25 | Python | 12,321 | 312 | from __future__ import annotations
import json
import os
import pathlib
import random
from typing import List
import matplotlib.pyplot as plt
import parse
import torch
from google.protobuf.json_format import ParseDict, MessageToDict
from loguru import logger
from matplotlib.patches import Rectangle
from ord_schema.pr... |
c8a755ddd477907a2b75b9e546f769f4e9cd41255b008d864cc1c48548b984cf | Python | 12,326 | 320 | import torch
from typing import List
import logging
import os
import Models.model_func as Model_Func
import pickle
from tqdm import tqdm
import yaml
class Univariate_Model(torch.nn.Module):
def __init__(self, device:torch.device):
super().__init__()
assert isinstance(device, torch.device), "devic... |
d6e85dbf97be089a67fab1f0b5a446cd70e96627fa93585e6e76585e5513abb8 | Python | 12,328 | 376 | # -*- coding: utf-8 -*-
#
# Auxiliaries used across all of Syncopy
#
# Builtin/3rd party package imports
import numpy as np
from numbers import Number
from copy import deepcopy
import inspect
import json
# Local imports
from syncopy.shared.errors import SPYValueError, SPYWarning, SPYTypeError, SPYError
from syncopy.s... |
fa6246c0e9ba41634d681b9eb06de323510fb8ab54e297393ef9639229cf1d1f | Python | 12,330 | 255 | import argparse
import logging
import random
import traceback
import NDATools
from NDATools import authenticate
from NDATools import exit_error
from NDATools.Configuration import ClientConfiguration
from NDATools.Utils import get_non_blank_input, get_int_input
from NDATools.upload.submission.api import CollectionApi
f... |
a98341022655c3642acf7bccaaa100beedd756d6dc7cb23b9fe247baf6ddd41a | Python | 12,331 | 385 | # 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... |
f409776e1313fab982657899de43a17ed5c23779c7d9abd28ee93c0d6dc8595f | Python | 12,332 | 308 | """
Script for extracting an analyzing a GraphMCF with a segmented membrane
Input: - A STAR file with a list of (sub-)tomograms to process:
+ Density map tomogram
+ Segmentation tomogram
- Graph input parameters
Output: - A STAR file with the (sub-)tomograms and their co... |
07f4c44554943f92aec24fe46e435988217cebfd0f99552bc6b518d4c8ef14dc | Python | 12,333 | 352 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import os,sys
import numpy as np
from dict2xml import createXML
# from string import split
def parsePV(filename):
"""
Parser fo... |
cd5551b6f4b39d3d0edb4b94ad4da85d189b3a467ff7a3ca22da3eeb6de568de | Python | 12,333 | 309 | """
Script for extracting an analyzing a GraphMCF with a segmented membrane
Input: - A STAR file with a list of (sub-)tomograms to process:
+ Density map tomogram
+ Segmentation tomogram
- Graph input parameters
Output: - A STAR file with the (sub-)tomograms and their co... |
96c4abba8601afd920acaf62be419f6928ce22661904e796517c7b6af3b1fc35 | Python | 12,342 | 213 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
# app specific libraries
import control.widgets as widgets
import control.camera as camera
import control.core as core
import control.m... |
af893b07796f943e3345fef4a5cb8c3df208a1e032508c0388dd0f82a98d5ac0 | Python | 12,345 | 409 | import os
import torch
from torch.hub import load_state_dict_from_url
from torchvision.datasets.folder import default_loader
from pathlib import Path
from torchvision import transforms
from .alexnet_gn import *
from .resnet import *
url_root = "https://visionlab-pretrainedmodels.s3.amazonaws.com"
def build_alexnet_... |
d72d812bc515dfcd8846fbcc38bfdc8096081921089f96b0bbbed981cd08b2e1 | Python | 12,349 | 257 | """
Script to run "add cancer" experiments. The general idea is to add cancers
in a particular order (either random or determined by cancer type similarity).
The prediction goal is the same as in 02_cancer_type_classification
experiments; that is, predicting presence/absence of a given mutation in
a particular cancer ... |
72075da40404fdfec378ec70550ef2ae18e4ccbbe4e80f259e499002b744962f | Python | 12,352 | 325 | """Classes representing parsed query expressions."""
from hed.models.query_util import SearchResult
class Expression:
"""Base class for parsed query expressions."""
MATCH_TERM = 0 # Bare term: ancestor search via tag_terms
MATCH_EXACT = 1 # Slash-path or quoted: exact tag match
MATCH_WILDCARD = 2 ... |
c5953b9bedf1bdee31701437b2b6167defce93614c686edc836a1b7bbbab5029 | Python | 12,352 | 291 | # Some of the code is referenced from below Github files:
# https://github.com/YudengLin/memristorBDNN, which includes `BDNN_Model.py` and `memristor_model.py`
from __future__ import division, print_function
import platform_4k
import torch
import torch.nn as nn
import numpy as np
class operation_paras():
... |
077603ef22eae0e070fa34d6449df3ec38211233b59c40d894e3df25c694bd1a | Python | 12,354 | 344 | """Schemas for VASP."""
from __future__ import annotations
import logging
import os
from pathlib import Path
from typing import TYPE_CHECKING
from ase.io import read
from emmet.core.tasks import TaskDoc
from monty.os.path import zpath
from pymatgen.command_line.bader_caller import bader_analysis_from_path
from pymat... |
0d22cb9b1f35d4743fc9bd8e405881c83dacbec565b72346f67f5fbc0a83d576 | Python | 12,354 | 289 | from collections import defaultdict
import numpy as np
import scipy
from pathlib import Path
from scipy.special import expit
from wsilearn.utils.asap_links import make_asap_link, make_link
from wsilearn.utils.cool_utils import Timer, is_iterable, mkdir, showim
from wsilearn.dataconf import DataConf, TrainType
from w... |
1f10c9fdd755d218f09b532d5d817140371afc98bdfc6801c9b30c5907def791 | Python | 12,354 | 270 | import copy
import os
import torch
import sys
sys.path.append('..')
from torch.utils.data import DataLoader
import data_utils
import utils
import torch.optim as optim
import torch.optim.lr_scheduler as lr_scheduler
import torchvision.transforms as transforms
import torchvision
import model_h_vector_embed_mean
import nu... |
eac4927b60be2c2080d9115f93fc37216b8706ccc0cf0753a05301c5ef138a19 | Python | 12,358 | 376 | from bokeh.models import Div
from bokeh.layouts import row, column
from bokeh.plotting import figure, show, output_file, save
import matplotlib.pyplot as plt
import numpy as np
from PIL import Image
import pandas as pd
def offset_pos(dataframe, n_policies=None):
if n_policies is None:
n_policies = dataf... |
4afec706307cc3cb16431dfdd570a740bd71f0840748f4c78c75b046a93051e4 | Python | 12,359 | 323 | """
General Classes for the package
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 15.09.15
"""
__author__ = 'martinez'
from pyorg.globals import *
# import graph_tool.all as gt
from .variables import *
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
try:
imp... |
9e7f548c134265bbafc1a474074fbae51169c67a6fbe73e8a0522ef67767026c | Python | 12,360 | 338 | """Module for agreement and consensus analysis between raters"""
from numpy import (arange, argmax, asarray, concatenate, diff, invert,
logical_and, maximum, mean, minimum, newaxis, ones, repeat,
sum, vstack, where, zeros)
from .. import Graphoelement
class MatchedEvents:
... |
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