sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7b7d3ab6c08cae03bf2ad6b1b2982d80f9bbd60abbd7596a76ab7da1fdcf90f5 | Python | 2,962 | 73 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Initialization of LFPykit
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This... |
4c18b28c310818e886d2990d13fc30310eb2c1a493f741cb827db36ec3d21b70 | Python | 2,963 | 62 | #####################################################################################################################
# Clone FastSurfer repo
git clone -q https://github.com/deep-mi/fastsurfer.git
cd fastsurfer
export FASTSURFER_HOME=$PWD
# Install python dependencies
python3 -m pip install --user --trusted-host pypi.... |
5f139c3656856ba8fb8956d77297b40200fbda306f945c5e82295a9a77eda1c1 | Python | 2,963 | 107 | # -*- coding: utf-8 -*-
import numpy as np
import h5py
from matplotlib import pyplot as plt
"""
Created on Wed Sep 13 14:36:22 2023
@author: alex
"""
# %%
def transformnet(stim_trans,net0,n):
net0i = np.int(net0*n+1)
net0i[net0i>stim_trans.shape[2]]=stim_trans.shape[2]
net0t = np.zeros... |
657449f7b3541bfa11c06def61440002e591aa1670a0f5543ecbb61e9e0f5a9b | Python | 2,963 | 84 | import torch
import torch.nn.functional as F
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.quant_utils import (
AsymmetricSignedQParams,
GlobalMinMaxObserver,
SimQuant,
)
from elasticai.creator.nn.integer.relu.design import ReLU as ReLU... |
e46196a89865cfcd96782731dc448b2e66951035a56649c7d93fb057bcd74b44 | Python | 2,963 | 97 | # -*- coding: utf-8 -*-
"""
Created on Tue Apr 13 18:51:40 2021
@author: divyoj
"""
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.animation import FuncAnimation
import numpy as np
import seaborn as sns
sns.set_style("whitegrid")
start=10;
stop=10;
step=1
def calculate_delta... |
e75c4f568081cf2cfce6c8dda700a004041464aa723c6648e1a63461ecd0756d | Python | 2,963 | 64 | #!/usr/bin/env python
## this script creates dataframes from the full similarity matrices for each movie and parcel
## and saves them to a new CSV file
## The dataframes contain the correlation values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Define the range for nodes
num_nodes = 210 ... |
7d6e296199fa39c1fa543b6b8103f8f1360b5564303e59ad1a70f4c183b03b72 | Python | 2,964 | 73 | import pandas as pd
import os
from cuppa.constants import MOCK_DATA_DIR
from cuppa.classifier.cuppa_classifier import CuppaClassifier
from cuppa.classifier.cuppa_prediction import CuppaPrediction, CuppaPredSummary
from cuppa.performance.performance_stats import PerformanceStats
from cuppa.visualization.visualization i... |
9622b209a1a5f69330f7df61c7ea1515ed1c63b228d246505ef1f1133dcf210e | Python | 2,964 | 100 | # pylint: disable=too-many-function-args, invalid-name
""" BSNIP ICA dataset loading script"""
import numpy as np
import pandas as pd
from omegaconf import DictConfig
from src.settings import DATA_ROOT
def load_data(
cfg: DictConfig,
dataset_path: str = DATA_ROOT.joinpath("bsnip/BSNIP_data.npz"),
indice... |
1d44a9f1751cd742fe9a4f18e882943f55462099eb81b8cd19f314ffd73721a7 | Python | 2,965 | 87 | from __future__ import print_function,division
import sys
import os
import numpy as np
import pandas as pd
import topaz.utils.star as star
name = 'coordinates_to_star'
help = 'convert coordinates table to .star file format'
def add_arguments(parser):
parser.add_argument('file', help='path to input coordinates ... |
50a292769188552c49d14f87b85ca4c03576d2a1406a3f1202241cb919af7357 | Python | 2,965 | 68 | # 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 torch
def flatten_graph(node_embeddings, edge_embeddings, edge_index):
"""
Flattens the graph into a batch size one (with dis... |
5cbb28658c2860acb1bb1264d79de714864549fe23f4b675d57d1d5f73e00813 | Python | 2,965 | 103 | import h5py
import numpy as np
import torch
from torch.utils.data import DataLoader, TensorDataset
import torch.nn as nn
import torch.optim as optim
import torch
import torch.nn.functional as F
from torch.optim import Adam
class VAE(nn.Module):
def __init__(self, latent_dim=30):
super(VAE, self).__init__(... |
e3f775c5ecb058aede0e80534a11ddb747208af437a717094f62dd02bac7269e | Python | 2,966 | 86 | import torch
import torch.nn as nn
import torchvision.transforms as transforms
from torch.utils.data import DataLoader, Dataset
import nibabel as nib
import os
import numpy as np
# Define the 3D AlexNet model
class AlexNet3DADClassify(nn.Module):
def __init__(self, num_classes=2):
super(AlexNet3DADClassify... |
8ca229ff7a178409498151407e59ffe8abbfb215f1c21da81f6098c91b52b0cc | Python | 2,967 | 65 | #!/usr/bin/env python
## this script creates dataframes from the similarity matrices
## (upper triangle) for each movie and parcel
## and saves them to a new CSV file
## The dataframes contain the correlation values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Define the range for nodes
... |
ee47dea2e8f285b2b7cab6703f737e85effa6a2d938d144de26bf89bc95dbb50 | Python | 2,967 | 83 | # 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... |
7f8146cf146d0f668781e819535f7f7edf30da67adada0867ac3a766df159fd0 | Python | 2,968 | 99 | """Calibration utilities for photoreceptor isomerization rates.
Port of calcIsomPerWatt.m and IsomerizationConverting.m
"""
from pathlib import Path
import numpy as np
# Physical constants
_PLANCK = 6.62607004e-34 # m^2*kg/s
_SPEED_OF_LIGHT = 299792458 # m/s
# Data directory
_DATA_DIR = Path(__file__).parent / ... |
b80c5c0c90bb87accf641f146d213d7643b255aacb0fbb285f55df845ba4272e | Python | 2,968 | 108 | """Command-line tool functionality.
Parses arguments and determines which tool should be called.
"""
import sys
import argparse
from abc import ABC, abstractmethod
from typing import Dict
import importlib
# New tools should be added to this list.
TOOL_NAME_LIST = [
'preprocess',
'train',
'denoise'
]
... |
c40fb9157b44ba239691adf34c9f0bd0e0e066af555664bdfadd3562d491b219 | Python | 2,968 | 98 | """Calculate and save number of trials for all recordings."""
from __future__ import annotations
import csv
import pathlib
from typing import Annotated
import mne
import mne_bids
import numpy as np
import pandas as pd
import pte
from pytask import Product
import motor_intention.project_constants as constants
OUT_DI... |
4d2f3cb0259fc5cf0be6bae9fb308db3350215974187231b0b76b424a16647a3 | Python | 2,969 | 77 | # 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... |
1d3aca110f1dd7adae25a5aa67777edd4449571b4ea516c9fbcd9b9f9253227d | Python | 2,970 | 70 | import argparse
import os
import pandas as pd
from constants import SCORE_COLUMNS
from tabulate import tabulate
_BASE_DIR = './results/lukas-final/'
_ML_PREDICTIONS_ROOT = _BASE_DIR + 'final-aug_01/rey-multilabel-classifier/'
_RG_PREDICTIONS_ROOT = _BASE_DIR + 'final-reg_01/rey-regressor-v2/'
_PRED_CSV_PATTERN = '{... |
4e7a14e7c907f69ebd24ac9b43ffdef55c5f2df106358ee05a397be9a01b6e53 | Python | 2,972 | 112 | import os
import numpy as np
import torch
import pickle
import scipy.io as sio
def mkdir(d):
"""only works on *nix system"""
if not os.path.isdir(d) and not os.path.exists(d):
os.system('mkdir -p {}'.format(d))
def _get_suffix(filename):
"""a.jpg -> jpg"""
pos = filename.rfind('.')
if po... |
76a7763917e7875a7516bcf6b327754f50d8bd633cdb8a004bd315d1304b46c3 | Python | 2,973 | 73 | # -*- coding: utf-8 -*-
r""" This package implements the louvain algorithm in ``C++`` and exposes it to
python. It relies on ``(python-)igraph`` for it to function. Besides the
relative flexibility of the implementation, it also scales well, and can be run
on graphs of millions of nodes (as long as they can fit in mem... |
94312e178353de447ff68c1ad891258cc7bafd12b1dd9f52ccf246bf3348e726 | Python | 2,973 | 110 | import yaml
import numpy as np
def load_config(config_path: str) -> dict:
""" Load configuration from YAML file. """
with open(config_path, 'r') as file:
return yaml.safe_load(file)
def cluster_signal(
signal_array: np.ndarray,
channel_list: list,
cluster_list: list
) -> np.n... |
c6101287d97f0a65240a9427c494acfc012d109df93281c64f8aeb51ba099683 | Python | 2,973 | 51 | #!/usr/bin/env python
#Likelihood calculaiton model
import pysam
from SCanSNP.VCFUtils import *
from SCanSNP.GenUtils import *
def ComputeLikelihood(vcf,GenotypesDF,Counts,DiffOnlyIndex):
'''
The ComputeLikelihood function calculates and sum up Altscores and Refscores of the possible mixed genotypes for every locu... |
2423f14fd7b7e5e1dcf93a7ca9a13c554be0388268e3c5196fdbbe128228c2d3 | Python | 2,975 | 71 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
479eb2fc3bd94f15a8426b8f2fc002ac68f3b3644a33c33a7ea6738660b3bb3e | Python | 2,975 | 80 | # 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... |
6b5b0c7186d9ae5ef76cac0b035e0a9729fdb8e0c8ba330001f001e127560a52 | Python | 2,975 | 104 | import numpy as np
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA
from sklearn.pipeline import make_pipeline
from mne.decoding import CSP
from help_funcs import load_exp_variables
from classification_pipelines import classify_feature
# ----- #
# Selection of classification hyperparamete... |
0b29d539fe0365d35330733ada505649c1e752a76a45c3d5b25f022de8a8300a | Python | 2,976 | 64 | #!/usr/bin/env python
## this script creates dataframes from the full similarity matrices for each movie and parcel
## and saves them to a new CSV file
## The dataframes contain the distance values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Define the range for nodes
num_nodes = 210 # 2... |
1d70195c92d903280e51dd603e06b2a89b9f184b0931e60bd29f0bd175ff33dd | Python | 2,976 | 99 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
SUITE_SAT14 = [
'barman-sat14-strips',
'cavediving-sat14-adl',
'childsnack-sat14-strips',
'citycar-sat14-adl',
'floortile-sat14-st... |
6df910ad9ba8ad9633d1b66cc5dce699f2e094dd20065cbe4a3c40fd3de4400b | Python | 2,976 | 99 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
SUITE_AGL14 = [
'barman-agl14-strips',
'cavediving-agl14-adl',
'childsnack-agl14-strips',
'citycar-agl14-adl',
'floortile-agl14-st... |
ccea062e6bc2af8be6d9d082a6622ff5a351941481f4bd4e1874cc71da5a82be | Python | 2,976 | 99 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
SUITE_MCO14 = [
'barman-mco14-strips',
'cavediving-mco14-adl',
'childsnack-mco14-strips',
'citycar-mco14-adl',
'floortile-mco14-st... |
feab3e55fbc8aa52b473cbf6be790affdc8d3318e221ca19a4732d3968a668a5 | Python | 2,976 | 72 | import lightning.pytorch as pl
import pandas as pd
from torch.utils.data import DataLoader
from dataset import TrainSeqDatasetProb, TestSeqDatasetProb
from training_config import TrainingConfig
class SeqDataModule(pl.LightningDataModule):
def __init__(self,
val_fold: int,
test_... |
227af4a621d137bbec7f22a46ddab91b167b0d4f0c1f370efd2b1f07c8d9bcb6 | Python | 2,978 | 92 | #
# Copyright Bradley Lowekamp
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed ... |
4514cffaed05ab9ddaf85b7c7d01ed879d8abf8f7554caf7b3c7fe4d0ce2305e | Python | 2,978 | 70 | from ..region_1020 import (FRONTAL_REGION_LIST, GENERAL_REGION_LIST,
HEMISPHERE_REGION_LIST)
from ..standard_1020 import STANDARD_1020_CHANNEL_LOCATION_DICT
from ..utils import (format_adj_matrix_from_adj_list,
format_adj_matrix_from_standard,
format_... |
4ee520df8677547a44d03bdfe18e7f264f22e3ae1a040b62bce1fbde094013c5 | Python | 2,978 | 73 | import torch
import torch.optim
import torch.utils.data
import torch.nn.parallel
from core.train import *
from core.test import *
from utils import *
from core.network import get_model
from loss import get_criterion
from datasets import get_dataloader
def main_worker(args):
args.logger = initialize_logger(args)
... |
81f0d4ab17f141af0fb175b25d60ddd138fd893e41bdc85aed61d73333dedea0 | Python | 2,978 | 99 | import torch
import numpy as np
import scipy.sparse as sp
from torch.nn import functional as F
def identity_mapping(x):
return x
activation_map = {
'relu' : F.relu,
'leaky' : F.leaky_relu,
'selu' : F.selu,
'sigmoid' : F.sigmoid,
'tanh' : F.tanh,
'none' : identity_mapping
}
... |
a4ec17e2e0b20e30b3c54786d1881e77ff5d99e7607eaf9ad70900ac01a49493 | Python | 2,978 | 98 | from typing import Optional
import jax.numpy as jnp
from netket.operator import AbstractOperator, ContinuousOperator
from netket.utils.types import DType
from netket.utils.numbers import is_scalar
from netket.vqs import VariationalState, FullSumState
from netket.stats import Stats
from tre_tvmc.driver.infidelity_psi.... |
ff1e9c5b26a34c7e021b66fa87366f76198065db48b4e8c3c89083a6f5653c2d | Python | 2,979 | 91 | # 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... |
bbe2c765db9fbbcde5a549502e8dd9bdb9a31d6d4b04768ca98c53d8d800dea5 | Python | 2,980 | 65 | #!/usr/bin/env python
## this script creates dataframes from the similarity matrices
## (upper triangle) for each movie and parcel
## and saves them to a new CSV file
## The dataframes contain the distance values for each pair of subjects.
import pandas as pd
from pathlib import Path
# Define the range for nodes
num... |
0c15c82331bddb9aa499c7be77ab8a8bd0ffa5a1356a210e9020b9664a434b60 | Python | 2,981 | 47 | """posthoc_histamine_2026-09-30.py (POST HOC, descriptive). SIGNCHECK flagged the lamina on 30 Sept as "a prediction to
test". Known answer: fly photoreceptors release histamine, which opens chloride channels on their targets (Hardie 1989;
Gengs et al. 2002) — an inhibitory synapse. The transmitter classifier has six c... |
ab7dda92c6f0fd0a24cd95c690a72847344c6c70adf3e776f2b4ed9e156e61e9 | Python | 2,981 | 78 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from downward.reports.compare import ComparativeReport
from common_setup import IssueConfig, IssueExperiment, is_test_run
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["issue717... |
ec89ec630af35c2f97cd4a0b212bd116f37828a570dac78e0e4f80bb348a24e1 | Python | 2,981 | 85 | #!/usr/bin/env python3
## this script creates dataframes from the full similarity matrices for each movie and parcel
## and saves them to a new CSV file
## The dataframes contain the correlation values for each pair of subjects.
import pandas as pd
from pathlib import Path
# ------------------------------------------... |
4839970d2467c8213cfca2d1f222270a12c9a88c56519cef65e0c23eaa864960 | Python | 2,982 | 94 | from torch import Generator
from torch.utils.data import DataLoader
from pathlib import Path
import pandas as pd
from ..prixfixe import DataProcessor
from .utils import BHI_preprocess_data, BHI_preprocess_df, BHIDataloaderWrapper
from .dataset import BHISeqDatasetProb
"""
230406 BHIDataProcessor added
- Target standa... |
8c8339981f74ad542c154ff3ef0891b69eceeb9384ef58af7b410ea2872fa51d | Python | 2,982 | 73 | ##this script takes in output from targetP, WPS and localiser and gives a list of proteins predicted to go to organelles
import os
import pandas as pd
def process_targetp(file_path):
df = pd.read_csv(file_path, sep="\t", comment='#', header=None, skiprows=2, usecols=range(7))
df.columns = ["ID", "Prediction",... |
4010315e64cba98ba89bc44e1d2eaefe06c2247c1e0a67b34929610707a4c092 | Python | 2,983 | 90 | #!/usr/bin/env python
import os
from deephe3 import testResultAnalyzer
prompt = '''
------------------------------------------------
# ============================================ #
# Analyzing Tool for DeepH-E3 Test Result #
# ============================================ #
Type in the numbers to choose an act... |
e80b8396342dbdff3d0d3354c9633b937a1494ffe5abbd0d53e20d28ab5e3816 | Python | 2,983 | 82 | """
Pygments
~~~~~~~~
Pygments is a syntax highlighting package written in Python.
It is a generic syntax highlighter for general use in all kinds of software
such as forum systems, wikis or other applications that need to prettify
source code. Highlights are:
* a wide range of common lan... |
0bd9bedb6e9aa9e9e0dab8186a2fdb678348e48f1532df6aa2e7c6698a675eae | Python | 2,984 | 110 | import numpy as np
import pandas as pd
from numba import njit
from sklearn import preprocessing
@njit(debug=False)
def get_row(v, row, n):
"""Extract a single row from a condensed distance matrix."""
values = np.zeros(n, dtype=v.dtype)
for j in range(n):
if row == j:
continue
... |
1adf1c1db5580af9e31287f470c0c69bde36a0df08b7ea8c7c5da7b79b4be9f7 | Python | 2,985 | 93 | """Tests for the _TerminalJobMixin heartbeat / watchdog logic."""
import os
import sys
import time
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
impor... |
4164b965c15b19091e30fe4a7e695d564a15e7e92b914f118aba888832673c83 | Python | 2,985 | 83 | """ Agent: Implementation of the forgetting model """
import numpy as np
from scipy.stats import beta
from random import choices
from en_utilities import safe_div
class Agent:
""" This class definition specifies the properties of the object that implements the forgetting model """
def __init__(self, agent_v... |
7a1d4bdab0d461be7f71572e9e69bb57c93fd9d9aa5c5ed5dbce176423b0f203 | Python | 2,985 | 72 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
7e767936f90a52f95f09ed970df79d00d849c70e1ad55f44f21caca27c4b8f8b | Python | 2,985 | 65 | #
# 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,... |
0469fb29e74fc1697b8d57cdfb8bb28b7f30457976102000c555f05febb9b120 | Python | 2,987 | 85 | """
https://github.com/MIPT-Oulu/Collagen/blob/master/collagen/modelzoo/segmentation/decoders/_unet.py
"""
import torch.nn.functional as F
from torch import nn
import torch
from model_utils.modules import Module
from model_utils.modules import ConvBlock
class DecoderBlock(Module):
def __init__(self, inp_channel... |
0b3a74fdb0e0d71145eee0c9ebbd8b2811b64816303060eeaa3c774615c1161b | Python | 2,987 | 80 | # 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... |
20c8a611bf226b57928eb7a1d6f9214746fd4e30c5ea6b49ef95d536bf3d02a2 | Python | 2,987 | 76 | from pathlib import Path
from typing import Any, cast
import torch
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.sequential.design_builder import SequentialDesignBuilder
from elasticai.creator.vhdl.design.design import Design
from .design import Sequenti... |
6bbc076e03a375924bd4195e2387caac429d125220503aded52a75e1f79da92c | Python | 2,987 | 90 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
b8da0ca78754329c5d996162acd4325d93e916fd3eed1b477cc172d4098f017f | Python | 2,987 | 66 | # Ultralytics YOLO 🚀, AGPL-3.0 license
import os
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = " "
import torch
from ultralytics.yolo.engine.results import Results
from ultralytics.yolo.utils import DEFAULT_CFG, ROOT, ops
from ultralytics.yolo.v8.detect.predict import DetectionPr... |
243d1951fa38d6c99e4fa796c854ca3cebdaa83d4bb70e0d22e034f66413ff5a | Python | 2,988 | 88 | from __future__ import print_function
import os
import numpy as np
import tensorflow as tf
import tflite_runtime.interpreter as tflite
from tensorflow.python.platform import gfile
# import pandas as pd
BOTTLENECK_TENSOR_NAME = 'pool_3/_reshape:0'
JPEG_DATA_TENSOR_NAME = 'DecodeJpeg/contents:0'
RESIZED_INPUT_TENSOR_NAM... |
555bf80e9169b33e1fcdbee2eae2743d34344b32eba2bcbffd6c6aef84a61520 | Python | 2,988 | 107 | """
Core recipes for EMT.
NOTE: This set of minimal recipes is mainly for demonstration purposes.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.emt import EMT
from quacc import job
from quacc.runners.ase import Runner
from quacc.schemas.ase import Summarize
if TYPE_C... |
643cced25c5022339b5c0528f9ac98a10d5c5f3568a6174ba7296b5b2974df93 | Python | 2,988 | 56 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
'''
Compute simplex counts of the full and E-E subgraphs of the original and manipulated connectomes.
Author(s): Daniela Egas S.
Last update: 11.2023
'''
import scipy.sparse as sp
import pandas as pd
import con... |
942c1c340a689a479ffc74c6a1cea0dec9d833566d5fa62f6b3130e2c6a830be | Python | 2,990 | 86 | from __future__ import annotations
import re
from typing import Any
from wikibaseintegrator.datatypes.basedatatype import BaseDataType
from wikibaseintegrator.wbi_config import config
from wikibaseintegrator.wbi_enums import WikibaseSnakType
class Lexeme(BaseDataType):
"""
Implements the Wikibas... |
b73e9517bb995f96ebb154eac0b4806851f294dfdb009470c231d875527e0087 | Python | 2,990 | 56 |
from sklearn.linear_model import LinearRegression
#from ..tools import regression
import numpy as np
def multregconn(activity_matrix, target_ts=None, parcelstoexclude_bytarget=None):
"""
activity_matrix: Activity matrix should be nodes X time
target_ts: Optional, used when only a single tar... |
e7e26e41c9de78d86f02ae9e28d036df3dcde110026c1742c42a21ee48d66e38 | Python | 2,990 | 67 | options = dict(
)
doc = dict(
__class__="""
Builds a Decision Tree (DT) on a preprocessed dataset.
"""
)
examples = dict(
categorical_encoding="""
>>> import h2o
>>> from h2o.estimators import H2ODecisionTreeEstimator
>>> h2o.init()
>>> prostate = h2o.import_file("http://s3.amazonaws.com/h2o-pu... |
5b4689eb48de1cf677a7c8800aaa844a3c443db89cc308c0bf0f7890d159f8dd | Python | 2,991 | 81 | import torch
import torch.nn as nn
from torch.nn import init
import math
from ..utils import _to_triple, _triple_same, _pair_same
class _ACSConv(nn.Module):
"""
Base class for ACS Convolution
Basically the same with _ConvNd in torch.nn.
Warnings:
The kernel size should be the same in the thr... |
09ddbcfb44876ac83fe3277e5039695de9ac6f03e7d4ce93a8cdbe929f66a206 | Python | 2,992 | 79 | # 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... |
4455f5eededf40bcdd75103e6b17bc5881f26d7a3734c38a333581a798cca358 | Python | 2,992 | 100 | from . import base
from . import functional as F
from ..base.modules import Activation
class IoU(base.Metric):
__name__ = "iou_score"
def __init__(self, eps=1e-7, threshold=0.5, activation=None, ignore_channels=None, **kwargs):
super().__init__(**kwargs)
self.eps = eps
self.threshold ... |
5079914b879acc19457f6ea1e05445a6a72e15d147bd2e8d192aa02a68fabfb6 | Python | 2,992 | 156 | import unittest
from parameterized import parameterized
from HyDGL.element_look_up_table import ElementLookUpTable
class TestElementLookUpTable(unittest.TestCase):
@parameterized.expand([
[
15,
'P'
],
[
86,
'Rn'
],
])
def... |
65e0d3cb6320b845ca3367166a1e8878322b4580ae773d6e2985317f1cddc7e3 | Python | 2,992 | 67 | """Regression test: the registration result viewer must load a custom-atlas
annotation in ANY supported format, not just NIfTI.
A custom 2D atlas can supply its annotation as the per-slice TIFFs written by the
coronal TIFF exporter. The viewer used ``load_nii_pir`` (nibabel only), which
raised ``ImageFileError: C... |
6de321a26079eea828d3e7d3af731acc951b0464f1eb7c3b442305f2f22949c6 | Python | 2,992 | 103 | from random import randint
import cocotb
import pytest
from cocotb.clock import Clock
from cocotb.triggers import RisingEdge
from elasticai.creator.arithmetic import int_arithmetic, int_converter
from elasticai.creator.testing import CocotbTestFixture, eai_testbench
from elasticai.creator_plugins.bram.utils import lo... |
d17c1b00a16b2dbd8a75cea0d28801d9e99803419cbd35d0e53f94c8921f3545 | Python | 2,992 | 104 | # Node-group asset "Outline Mask" (ShaderNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING
fr... |
575f0c897294cc1bb3262018901f737fa1dac8e56a5d91d3ebea2cf7e929d6c7 | Python | 2,995 | 76 | extensions = dict(
extra_params=[('verbose', 'FALSE')],
set_required_params="""
parms$training_frame <- training_frame
args <- .verify_dataxy(training_frame, x, y, autoencoder)
if( !missing(offset_column) && !is.null(offset_column)) args$x_ignore <- args$x_ignore[!( offset_column == args$x_ignore )]
if( !missi... |
1b2d8225a6cc4f6b4f9975c17990a21842b79748c976af6de4b0e7d1e5ee9cb4 | Python | 2,996 | 83 | # -*- coding: utf-8 -*-
"""
Created on Thu Oct 21 11:54:57 2021
@author: CY
"""
import torch
from torch import nn
import torch.nn.functional as F
import copy
class ProjectorHead(nn.Module):
def __init__(self, in_channels: int, hidden_size: int, out_size: int):
super().__init__()
... |
30fe6530cea147c18f701a44b06af68b96ea1fd66e6f6484679aeef45b77fabb | Python | 2,996 | 103 | from __future__ import annotations
from types import SimpleNamespace
import pytest
from quacc import job
from quacc.wflow_tools.customizers import customize_jobs, update_parameters
def test_customize_jobs():
def add(a, b=1):
return a + b
def mult(a, b=2):
return a * b
jobs = customize... |
497fb3d7808b89a3485e2e056b5d2ef895d07df9f172807422e2fa9dbe65366f | Python | 2,996 | 73 | """The char_set and code_point keys travel from the error call onto the issue dictionary."""
import unittest
from hed.errors.error_reporter import ISSUE_DETAIL_KEYS, ErrorHandler
from hed.errors.error_types import ValidationErrors
class TestIssueDetailKeys(unittest.TestCase):
def test_string_level_error_carries... |
9ef6a7d03f2ce21f0a32f9a0e1f9e50170cc73942e7c28780f3d311a4a9cf776 | Python | 2,996 | 95 | ##
# \file MotionSimulator.py
# \brief Abstract class to define interface for motion simulator
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date September 2017
#
# Import libraries
import os
import numpy as np
import SimpleITK as sitk
from abc import ABCMeta, abstractmethod
import pysitk.p... |
ef9fd340725a85bdd1e6a67ec4a242af2e37b32a618cd048a576e6ca950791a8 | Python | 2,996 | 63 | from src.models.other_models.resnet import *
from src.models.other_models.resnetV2 import resnet18V2
from src.models.other_models.shallow_cnn import *
from src.models.rey_regressor import *
from src.models.other_models.efficientnet import *
from typing import *
import torch.nn as nn
def get_architecture(arch: str,
... |
28f1b95afa1326a8c009c0845afd28adc331d85cb549462bf1ad9534f2226507 | Python | 2,997 | 117 | import matplotlib.pyplot as plt
import numpy as np
import meep as mp
resolution = 40 # pixels/μm
Si = mp.Medium(index=3.45)
dpml = 1.0
pml_layers = [mp.PML(dpml)]
sx = 5
sy = 3
cell = mp.Vector3(sx + 2 * dpml, sy + 2 * dpml, 0)
a = 1.0 # waveguide width/height
k_point = mp.Vector3(z=0.5)
def parallel_wavegui... |
b8502783983868b0d68def243478e1ef3e7b3d7e3f8766a718715dfaef43b126 | Python | 2,998 | 101 | # 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... |
d7c6ee734b8dae3539c265b2253481b04c802b5958585770325f9c785c550e1b | Python | 2,999 | 117 | """Protocol definitions for HDL abstraction.
This module defines the protocols (interfaces) that all HDL implementations must follow.
Using Protocol classes allows for structural subtyping (duck typing with type checking).
"""
from abc import abstractmethod
from collections.abc import Iterator
from typing import Any,... |
0706f1fea26b8368a6fde7746ff310199e40698105c3449fd47267bd0ee1deeb | Python | 3,000 | 96 | # Utilities for MRI postprocessing
#
# Copyright (C) 2014 David S. Smith
#
# 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 2 of the License, or
# (at your option) any later ver... |
939c56065fd8dcea1ad9c72ba6feea712dd9df11bdc80d7be3e3bdcc62d143bd | Python | 3,000 | 98 | from __future__ import annotations
import json
from typing import Any
from wikibaseintegrator.models.basemodel import BaseModel
from wikibaseintegrator.models.claims import Claims
from wikibaseintegrator.models.language_values import LanguageValues
from wikibaseintegrator.wbi_enums import ActionIfExists
... |
3f1243d2cff9370a95a39bd49080849944b7d829d9e15c1b6e3387e8b30cbfa3 | Python | 3,001 | 93 | # flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
bd740790c02afa3314cade80287d3c82cf7495c64a2bd18de93c66cee3fc0aef | Python | 3,001 | 103 | import sys
from os.path import expanduser, join, isfile
import threading
from tornado import web, ioloop, httpserver
from sockjs.tornado import SockJSConnection, SockJSRouter
import json
from collections import OrderedDict
import numpy as np
clients = set()
n_messages = 0
def read_points(fn):
if isfile(fn):
... |
ca190c70ae5b5f4501c9bf7edd1411a2a4c0168367cfd334cd0a26316dd4388d | Python | 3,001 | 81 | """Constants used for the"""
from hed.schema.hed_schema_constants import HedSectionKey
# These are only currently used by the XML reader/writer, but that may change.
XSI_NAMESPACE = "http://www.w3.org/2001/XMLSchema-instance"
NO_NAMESPACE_XSD_KEY = f"{{{XSI_NAMESPACE}}}noNamespaceSchemaLocation"
NAMESPACE_XSD_KEY = f... |
08e39e4a8c6e5e441505366c4465a0d17e0ccbc2329151a039cb139581c40836 | Python | 3,002 | 88 | """Implements a Gaussian mixture model, in which parameters are fit using
gradient descent. This example runs on 2-dimensional data, but the model
works on arbitrarily-high dimension."""
import matplotlib.pyplot as plt
from data import make_pinwheel
from scipy.optimize import minimize
import autograd.numpy as np
imp... |
f7ff31838a537724c7bd593845191c1c181d49ef3fddcfca20b8d4170900e606 | Python | 3,003 | 82 | # 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... |
fceac232e380f1e76f722876a3cd3497365bf8761d98a9941110a808df6ca6a8 | Python | 3,003 | 108 | import itertools as it
import warnings
import autograd.numpy as np
import autograd.numpy.random as npr
from autograd import grad, value_and_grad
from autograd.test_util import check_grads
rs = npr.RandomState(0)
def arg_pairs():
scalar = 2.0
vector = rs.randn(4)
mat = rs.randn(3, 4)
mat2 = rs.randn(... |
8c37bcdf3da4787ea20fb6c5c4c5ba4ce9c1d3e737617b1e39a80d08ba77f257 | Python | 3,007 | 118 | #!/usr/bin/env python
#******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... |
b4a3f8aa1521c6ee35b5c565044675f71a84c2d7e416cd4c639aed3ada726e4d | Python | 3,007 | 58 | # 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... |
19e3f33a911d00757a2650c2c5f1ccb203baa29969336d01d966a629a538925c | Python | 3,008 | 94 | import os
import random
from time import time
import pandas as pd
import numpy as np
import networkx as nx
import argparse
import pickle
import math
from utils.utils import *
from utils.graph_creation import *
from utils.motif_counts import *
from utils.visualization import *
import graph_tool.all as gt
sns.set_conte... |
129eecb04fb1ec1d6820871cf1bc70182cfb4dd304af2674b4e8085732b1e2bc | Python | 3,009 | 46 | # -*- coding: utf-8 -*-
import argparse
from supar import CRFDependencyParser
from supar.cmds.run import init
def main():
parser = argparse.ArgumentParser(description='Create first-order CRF Dependency Parser.')
parser.set_defaults(Parser=CRFDependencyParser)
parser.add_argument('--mbr', action='store_t... |
b9fd60ac3e28d510e405926c922c71a3a6218058be54218a1f0bfb873c2461b5 | Python | 3,009 | 74 | # -*- coding: utf-8 -*-
import argparse
import sys
def parse_args():
argparser = argparse.ArgumentParser()
argparser.add_argument(
"domain", help="path to domain pddl file")
argparser.add_argument(
"task", help="path to task pddl file")
argparser.add_argument(
"--relaxed", des... |
d9a16a4683415bca65d4253eaab2ef208dc8d3a8c772309982db841a981cceb2 | Python | 3,009 | 110 | # 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... |
0a547b30bf2ece43968a194901877b7131ada5aee45e9ccad2fefe31a954e502 | Python | 3,010 | 107 | from dataclasses import dataclass
import torch
from torch.nn.parameter import Parameter
from elasticai.creator.base_modules.linear import Linear, MathOperations
from elasticai.creator.base_modules.math_operations_torch import TorchMathOperations
from tests.tensor_test_case import TensorTestCase
def tensor(data: lis... |
9e24ab58e3b739f50ae016166d5ab2ddafca0b3a5379982417f986a932030d39 | Python | 3,010 | 88 | from __future__ import annotations
import re
from typing import Any
from wikibaseintegrator.datatypes.basedatatype import BaseDataType
from wikibaseintegrator.wbi_config import config
from wikibaseintegrator.wbi_enums import WikibaseSnakType
class Sense(BaseDataType):
"""
Implements the Wikibase... |
f154b4a5a2ef2f86f32ab10e45448be58fb69d3d66ac96f3b359da93b9cfdd4b | Python | 3,010 | 80 | import matplotlib
matplotlib.use("Agg")
import torch
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
from utilities.script_func import init, post, ScikitFeat_pre
import pickle
import logging
logging.info("")
def main():
import Models.models as Models
import Models.model_func as Model_Fu... |
99eb8f14848db74768667d7706b39bfe3ce73f954b01ee8720b134738f8dcc48 | Python | 3,011 | 105 | # Node-group asset "Slice Edge Instances" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_C... |
9c67b84a1546b176f7a910fb87731dfecd15a6813978d3badf11542d68ee258e | Python | 3,014 | 92 | # 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... |
a6713d3082cd19db9338d7291877e14d812b2733f3b965a8a255ece50a7d6c07 | Python | 3,014 | 95 | from __future__ import annotations
from typing import TYPE_CHECKING
import jax.numpy as jnp
from flax import linen as nn
if TYPE_CHECKING:
import jax
import jaxlib
class FlaxEncoder(nn.Module):
n_latent: int = 10
n_layers: int = 2
n_hidden: int = 800
dropout_rate: float = 0.1
latent_dis... |
c17883c48e418a7052c15fadefe7f4f6d46232087b3eb5f554b3cd1b148714e3 | Python | 3,014 | 46 | # -*- coding: utf-8 -*-
import argparse
from supar import CRF2oDependencyParser
from supar.cmds.run import init
def main():
parser = argparse.ArgumentParser(description='Create second-order CRF Dependency Parser.')
parser.set_defaults(Parser=CRF2oDependencyParser)
parser.add_argument('--mbr', action='st... |
0b3b3619e3ba436eda31778b61b2e7a2e290109f541c1ed88dd67080d84a5efd | Python | 3,016 | 76 | #! /usr/bin/env python3
import os
import subprocess
import logging
import APT_interface
class cd :
"""Context manager for changing the current working directory, and automagically changing back when done"""
def __init__(self, path):
self.path = path
def __enter__(self):
self.old_path = ... |
0d19528a68364c859cfbd427099f74c83014d6c85f12548f57bb36aa5ae5ff9e | Python | 3,016 | 76 | #
# 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,... |
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