sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cc25d5ea8e520e90afbb04c27d01a4e6bdf580391d5843e17c26848083402583 | Python | 3,751 | 105 | import unittest
import numpy as np
import numpy.testing as npt
from reinvent.models.reinvent.models.vocabulary import Vocabulary
from tests.test_data import SIMPLE_TOKENS
class TestVocabulary(unittest.TestCase):
def setUp(self):
self.voc = Vocabulary(tokens=SIMPLE_TOKENS)
def test_add_to_vocabulary... |
047259f8f1037ee3faffe7668a66acae5bc580b06fbed5ed6155813b285ba034 | Python | 3,753 | 112 | from sklearn.cluster import KMeans
from sklearn.metrics import silhouette_score,calinski_harabasz_score,davies_bouldin_score
from sklearn.metrics import adjusted_mutual_info_score, adjusted_rand_score, average_precision_score, roc_auc_score
import numpy as np
import community as cm
import networkx as nx
#import tensorf... |
f4b8450a753f2a64c910efd11b08fc7197c5bc13de02af00572f1732c8302dce | Python | 3,754 | 98 | import os
import torch
def xpu_device_index(local_rank: int) -> int:
"""
Map a local rank onto a visible XPU device index.
Under ZE_AFFINITY_MASK each rank sees a single tile, so local_rank can
exceed the number of visible devices; torch then rejects the index with
"value cannot be converted to ... |
fbc4781d035f1fde2d431d5768e799c07a051102eab8024a936d81f4a4d9ad0b | Python | 3,755 | 107 | from typing import Dict, List, Optional
import torch
from e3nn.util.jit import compile_mode
from mace.tools.deprecation import warn
from mace.tools.scatter import scatter_sum
@compile_mode("script")
class LAMMPS_MACE(torch.nn.Module):
def __init__(self, model, **kwargs):
super().__init__()
warn(... |
b700e7e1945083051286300a489845739e8207731d65ad0bae11ef1976ff0b3e | Python | 3,759 | 74 | __author__ = 'palmer'
import argparse
import numpy as np
def centroid_imzml(input_filename, output_filename, step=[], apodization=False, w_size=10, min_intensity=1e-5, prevent_duplicate_pixels=False):
# write a file to imzml format (centroided)
"""
:type input_filename string - source file path (must be .... |
ebbf43e002d0ea1c79bfb5f8f03de1fef8b01009ca9f4777ab80aa6441019af5 | Python | 3,759 | 74 | import numpy as np
import pandas as pd
import os
import pickle
if __name__ == "__main__":
hcp_sessions_list = ['REST1_LR', 'REST2_LR', 'REST1_RL', 'REST2_RL']
cv_sessions_list = ['LR_S1', 'LR_S2', 'RL_S1', 'RL_S2']
# to save subject ids and head motions across sessions to files
output_path = 'PROJECT... |
7c2f2fa5f22a153b531730a13eaf8b9dedd6f9abf70b985e0578b48ab25960b0 | Python | 3,764 | 103 | # 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... |
c7f15d7d1932627eaf56d1f1ffd55e1962e4cc77896751ffbf4d39aaf018d250 | Python | 3,765 | 85 | from torch import nn
import torch
from transformers import AutoImageProcessor, SwinModel
import torch
import cv2
from copy import deepcopy
from transformer import *
from position_encoding import *
class BioTransformer(nn.Module):
def __init__(self, num_classes,d_model=768,nhead=8,num_decoder_layers=6, dim_feedfor... |
c90d84117774dd8a57b9c51e45b5d8b1c9c22a80534db560cc521c3608b9bfe3 | Python | 3,766 | 113 | import os
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.axes import Axes
from matplotlib.colors import Colormap
# Make subpackage plotting tools also available
from .graph._visualization import *
from .image._visualization import *
from .utils import _calc_plot_dim
def plot_input(X: np.ndarray,... |
2a2ab65b735faec12b43f633c2d4d3a6e3ed4f76d1a1a7083ee9b2bafe936eda | Python | 3,767 | 120 | # Copyright (C) 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
import jax
import keras
class CNNModel(keras.Model):
def compute_loss_and_updates(
self,
trainable_variables,
non_trainable_variables,
... |
1ed3708121b3cc435c2b4706790c8af7ded9fda5e943bfbc3058304be7bd53f9 | Python | 3,768 | 114 | # Copyright (C) 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
Base classes for Federated Analytics.
This file can serve as a template for creating your own Federated Analytics experiments.
"""
from openfl.federated.task.runner import TaskRunner
from openfl.utilities import TensorKey
from openfl.u... |
d6672a06f428c579a5dd95a0001cdf90d13d77c4e2d41d4d5d9dd0f53e3d766f | Python | 3,772 | 103 | # 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... |
64d6d4bee9c5cd30e78d7258fc8a9ba586b9f86e82e267d71f0744d358537695 | Python | 3,775 | 125 | import unittest
import numpy as np
from fimpy.roi_extraction.local_correlations import grow_rois, correlation_map
from fimpy.roi_extraction.anatomical import extract_traces_around_points
def test_positive_corr():
video = np.array(
[
[
[[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1... |
d1213f6eda31bcb65d300210a6e3b42cc50af16e4da7b56167b3200fcde4a52f | Python | 3,776 | 118 | from __future__ import annotations
import argparse
import sys
from typing import (
TYPE_CHECKING,
Any,
Callable,
Generic,
Iterable,
TypedDict,
TypeVar,
overload,
)
from typing_extensions import Required, TypeAlias, Unpack
if TYPE_CHECKING:
from argparse import _SUPPRESS_T, _Action... |
329246d99fa699109a7317ee93270822c8d8605729c89892a19e8fb1b47a6d65 | Python | 3,777 | 99 | #### make_image_from_bin.py
# Copyright (C) 2010 R. Cameron Craddock (cameron.craddock@gmail.com)
#
# This script is a part of the pyClusterROI python toolbox for the spatially
# constrained clustering of fMRI data. It converts a NPY file generated by
# binfile_parcellation.py, group_binfile_parcellation.py, or
# group... |
c0ea54047264cdc54d90b60e7d78eae5ecb3843dcc52ccfb70346f12105c1ae9 | Python | 3,779 | 141 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""PKI CLI."""
import logging
import os
import sys
from pathlib import Path
from click import Path as ClickPath
from click import echo, group, option, pass_context, password_option
from openfl.utilities.ca.ca import (
CA_CONFIG_JSON,... |
2d973d343e4383e262fc8b2dfb7af735b4c97c50913d9570c67ce37437f3dfbf | Python | 3,780 | 110 | # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
b7bbbcaa06ba1cbfd82aeed879e93b10f8c16c1c76d7308bf34fd14c3e3730a2 | Python | 3,784 | 104 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
4393cea2c5f17090b87dcfaae8e0e8ae836f4ae6396c599f201c734cde92ef62 | Python | 3,786 | 123 | import os
from pathlib import Path
import re
import openpyxl
from openpyxl.styles import Font
import csv
import codecs
import sys
import argparse
import subprocess
import io
def generate_unique_id(base_id, id_list, num):
num_list = []
split_base = base_id.split(":")
split_base_num = int(split_base[1]) + nu... |
8ad6e62cdc4a2b86c94053145fb2f96abbf43b0a1ffc7e1e122a4f2f3350e372 | Python | 3,786 | 124 | """Checks and associated errors."""
import math
import geomstats.backend as gs
def check_integer(n, n_name):
"""Raise an error if n is not a > 0 integer.
Parameters
----------
n : unspecified
Parameter to be tested.
n_name : string
Name of the parameter.
"""
if n is not No... |
39aea124058de6c8e91bec44364b76b7b513fb28f3e5681b3029965914d95f65 | Python | 3,787 | 112 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import matplotlib.pyplot as plt
import numpy as np
import pickle
# use this format to tell the parsers
# where to insert certain parts of the script
# ${imports}
def chunks(lst, n):
"""Yield successive n-sized chunks from lst."""
for i in rang... |
c176882bceaacb602f9e372a39b7175fae71374a6613e7bf99a67367933b37e7 | Python | 3,787 | 139 | """Run K-medoids on manifolds for K=2 and Plot the results.
Two random clusters are generated in separate regions of the
manifold. Then K-medoids is applied using the metric of the manifold.
The points are represented with two distinct colors. For the moment
the example works on the Poincaré Ball and the Hypersphere.
... |
3994ebd909581f4f262ccec9cc69b25efc5e551e9e2ffd969855553f05a51151 | Python | 3,789 | 118 | # pylint: disable=protected-access, redefined-outer-name
from __future__ import absolute_import
import copy
import sys
from argparse import ArgumentParser
from os import PathLike
from pathlib import Path
import pytest
from configargparse import Namespace
from pytest_mock.plugin import MockerFixture
from snakebids.cl... |
8a15b4972a9f3e10e9269d8ebf4b3c3907582351a39af83df735661c5ffac233 | Python | 3,793 | 86 | import os
import argparse
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
parser = argparse.ArgumentParser()
parser.add_argument('--run1', '-r1', type=str, default=None, required=True)
args = parser.parse_args()
sbs_mapped_arr = np.load(os.path.join(args.run1,'sbs_mapped_arr.npy'))
R_mean = np.... |
8c6e7ccac3c92c75b925c096d6b4b275e20649ef583a33ec8fe213a25667e602 | Python | 3,794 | 114 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
import os
from nequip.nn.compile import ListInputOutputWrapper, DictInputOutputWrapper
from nequip.data import AtomicDataDict
from nequip.data._key_registry import get_dynamic_shapes
from ... |
62abefaeecac62a3fd7ce93f6a0b6f9cbff215c84247c2e1dc74bca681886987 | Python | 3,795 | 101 | """A collection of constants for testing"""
SIMPLE_TOKENS = {
t: i
for i, t in enumerate(
["$", "^", "(", ")", "1", "2", "3", "=", "C", "F", "N", "O", "S", "c", "n"]
)
}
PARACETAMOL = "CC(=O)NC1=CC=C(C=C1)O"
SCAFFOLD_SUZUKI = "Cc1ccc(cc1)c2cc(nn2c3ccc(cc3)S(=O)(=O)N)[*]"
INVALID = "INVALID"
NONSE... |
4939d40de2daecdbecd40fa4f81f119a27a33903e1f9524636cfbc450300d03a | Python | 3,796 | 106 | """Pure path-resolution helpers for MNI template files.
Resolves logical (template, resolution, file_type) tuples to local paths.
Files are fetched on first use from the `nltools/niftis` HF dataset; see
`nltools.templates.fetch`.
"""
from .fetch import fetch_resource
from .registry import SUPPORTED_RESOLUTIONS, VERSI... |
bd7fa652a88077bb0dc9acc01bdcb1317314c3a2172bf3d9b40a3346430c0e19 | Python | 3,796 | 110 | import json
import click
from corgie.log import configure_logger
from corgie.log import logger as corgie_logger
from corgie.argparsers import corgie_option, corgie_optgroup
from corgie.data_backends import get_data_backends, str_to_backend, \
DEFAULT_DATA_BACKEND, DataBackendBase
from corgie.cli.downsample im... |
ee2522848f6b7fb5afc8c7d4e0cf40f8920f1bf603b8c1c79d1b4e773bef4aa6 | Python | 3,797 | 115 | """Centralized filesystem paths used by SanPy."""
from __future__ import annotations
import shutil
import sys
from pathlib import Path
from platformdirs import user_documents_dir
from sanpy.sanpyLogger import get_logger
logger = get_logger(__name__)
class SanPyPaths:
"""Build and initialize SanPy's bundled a... |
b8c7d870573c3927759d7e3c72adc2db7a11003902b890bd2a7b95524356d843 | Python | 3,798 | 126 | #!/usr/bin/env python
import os
import sys
import matplotlib.pyplot as plt
import nibabel as nib
import nilearn.image as nimage
import numpy as np
import pandas as pd
import seaborn as sns
import scipy.linalg as la
from glob import glob
from budapestcode.utils import compute_tsnr
from budapestcode.viz import make_mo... |
13e69005b0f8d6490645138bab9078aaf1941f42fcaf2045b6965474a43a08da | Python | 3,801 | 93 | import argparse
import sys
from Utils.fileconverter import itk_to_nrrd
from Engine.train import initiate as train_initiate
from Engine.evaluate import initiate as evaluate_initiate
from Utils.MSD_utilities import generate_training_data
from Utils.plot import plot_train_data
from Utils.PETCT_LungDx_utilities import con... |
423f33c09a6a99cfcff81f95c92d754623698dee8155a26470bc3d546cc521d8 | Python | 3,805 | 104 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
from logging import getLogger
import numpy as np
from torchvision import datasets, transforms
logger = getLogger(__name__)
def one_hot(labels, classes):
"""
... |
452d56af365da8a8748187e8b6122ae032b8e30ab4998b8f2f1375ce6d4da804 | Python | 3,806 | 88 | """Check TCREmp stages across fresh processes and Linux CPU allocations.
Uses generated productive junctions, no assay data or stored fitted state. Each
invocation re-embeds and refits through the production entry point.
"""
from __future__ import annotations
import argparse
import faulthandler
import hashlib
import ... |
53acbb9c645c404d299efca863516291a9f810d5dbe360dc3c258c311ced49bf | Python | 3,809 | 84 | # import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import numpy as np
class CUBA_LIF_network:
def __init__(self):
self.main_Path = os.getcwd()
self.dataPath_TRAIN = self.main_Path + '/train_data'
self.netPath = self.main_Path + '/netwo... |
022c2030cfa07fe46abac898c84de1aabc108fdf887f7253efdeaea4d07dcae2 | Python | 3,811 | 120 | # -*- coding: utf-8 -*-
import numpy as np
from sklearn import preprocessing
import copy
from scipy import signal
def standardize_transients(transients, method='standard'):
if method == 'standard':
scaler = preprocessing.StandardScaler().fit(transients)
elif method == 'quantile':
scal... |
527ba0676552bc47330e22339d8be75c5e7b0c774c71bb0a5bd5fd77acdc2206 | Python | 3,814 | 112 | import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
import sys
sys.path.append('/n/groups/marks/users/david/github/pareSingleLibrary2/codebase/pairedEnd/ex62_gvp/')
import importlib
import dataTools as dt
importlib.reload(dt)
import regressionTools as rt
importlib.reload(rt)
from regressionToo... |
80661d4c1a9a8ca246c7cf05ef40c40341f188742b3e776c3a03870c4f37a5c6 | Python | 3,814 | 102 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
88dabbb480f90bc5217d2d1167aec820b248257f8f391840de8d13aa0b64e202 | Python | 3,814 | 101 | import torch
from torch.utils.data import DataLoader
from torch import optim, nn
from dataset import MultiModalDataset
from model.classifier import ClassifierModel
from torch.utils.data import DataLoader, random_split
# Replace these with your actual data paths and labels
face_image_paths = ['path/to/face/image1.jpg'... |
daf69922efa19819a254989488b13bfe72bcf08354d15d519079b4a4468e3cd2 | Python | 3,816 | 106 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
from logging import getLogger
import numpy as np
from torchvision import datasets
from torchvision import transforms
logger = getLogger(__name__)
def one_hot(labe... |
d3aff35c2b5a9dec78c9bd4440b6345e1346a1e9164ad959174ee8a9d10d66fd | Python | 3,820 | 87 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cogn... |
15fcb464d27713ac8934d478bd1a5ce69a24c7b020612ef7cfb2ad5c57517c89 | Python | 3,823 | 131 | # Copyright (C) 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Director CLI."""
import logging
import sys
from pathlib import Path
import click
from click import Path as ClickPath
from click import group, option, pass_context
from dynaconf import Validator
from openfl.experimental.workflow.comp... |
173768b610acc3b24e77d52ad59131821682ece857b138a87b340c2d20291959 | Python | 3,825 | 80 | import sys
import numpy as np
from neurolib.models.aln import ALNModel
from neurolib.utils.loadData import Dataset
import matplotlib.pyplot as plt
from nest_elephant_tvb.utils import create_logger
def run_example(co_simulation, path="", simtime=100,
level_log=1, resolution=0.1,
time_syn... |
d812c2426214e820f268407f4b5e38cecb98d4aba22609f60d5c870a4f0db60f | Python | 3,825 | 158 | # -*- coding: utf-8 -*-
"""
The main module. Start all system components and shutdown gracefully.
Author: Tal Eisenberg, 2021
"""
import multiprocessing
import os
import threading
import logging
import flask
import flask_cors
from flask_socketio import SocketIO, emit
import json
import sys
import argparse
from dotenv ... |
32ac0be9081e5f5cf077e3ffcea2a15b5f32f75a38349fd73b699c689240977c | Python | 3,826 | 137 | import inspect
import numpy as np
import pytest
import geomstats.backend as gs
# TODO: remove backend influence
# TODO: simplify most of this
def autograd_backend():
"""Check if autograd is set as backend."""
return gs.__name__.endswith("autograd")
def np_backend():
"""Check if numpy is set as backen... |
872b1f3dd6e58692ec281f9752adaaee31474232ae347fee41c5861ee4b834ea | Python | 3,834 | 119 | import numpy as np
import cv2 as cv
from ctypes import c_int, pointer
import image_observers.YOLOv4.darknet as darknet
import bbox
class YOLOv4Detector:
"""
Bounding box detector using the YOLOv4 algorithm, based on the paper
"YOLOv4: Optimal Speed and Accuracy of Object Detection"
Code from: https://... |
c36dec28cd483caadb129810e478a53bc4ac04fd5c5709708dec832fd2a0873d | Python | 3,834 | 102 | '''
Module focused on the implementation of Auxiliary Convolutional Layers
'''
import torch.nn as nn
import torch.nn.functional as F
class AuxiliaryConvolutions(nn.Module):
"""
Additional convolutions to produce higher-level feature maps.
see the original paper where SSD300 is implemented for further
... |
efefea88a8f1b707a11c16f27e79418fead7ae4e68c133d5fdaae176f7ba2ecb | Python | 3,834 | 111 | from geomstats.test.data import TestData
from .base import LevelSetTestData
from .fiber_bundle import FiberBundleTestData
from .quotient_metric import QuotientMetricTestData
from .riemannian_metric import RiemannianMetricTestData
class PreShapeSpaceTestData(LevelSetTestData):
def is_centered_vec_test_data(self):... |
e84cd28d16dc156d18ad017bde8c2dc9b42f7fc5ad0aa7c74b9d66ac2a9cfd00 | Python | 3,835 | 106 | import pytest
import geomstats.backend as gs
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.general_linear import SquareMatrices
from geomstats.geometry.special_euclidean import (
SpecialEuclidean,
homogeneous_representation,
)
from geomstats.test.random import LieGroupVectorRandomD... |
fdcbad33866c6408cb11c29d291f08b5c809a0701c3107166cc7764651dac791 | Python | 3,835 | 122 | import os
import argparse
import warnings
warnings.simplefilter(action="ignore", category=FutureWarning)
import pandas as pd
import tensorflow as tf
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
from activation_models.generators import get_activation_models
from custom_model_tools.manifold import (
... |
764a962b28233e3576f08474e0490f34c7b1fbd1efbe7e9758731a3a89e11f33 | Python | 3,836 | 123 | # Tests the CustomResourceMemberlist provider
from dataclasses import asdict
import threading
from chromadb.test.conftest import skip_if_not_cluster
from kubernetes import client, config
from chromadb.config import System, Settings
from chromadb.segment.distributed import Memberlist, Member
from chromadb.segment.impl.d... |
fecaf047c7f9a2e0724c8c258ca25ef0cf68cf512b9624abe8a153725f11ce63 | Python | 3,838 | 98 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cogn... |
38be8e2926cdf03d5c531ec375d001fe7450a6f11e8a6671c725b7876bdabfcc | Python | 3,839 | 142 | """
Functions for querying or mutating values in arbitrarily nested dictionaries and lists.
Author: Tal Eisenberg, 2021
Each of the functions in this module are "path functions" - f(d, path), where d is a
collection, and path is either a string key, an int index, or a tuple representing
a path in the collection. A pat... |
6a178172c3be1e333681c678cf178b4db78bde4a81f9052e2698fb8117ddbe71 | Python | 3,840 | 134 | """Hardwre reporting"""
from __future__ import annotations
import platform
import subprocess as sp
import logging
from typing import Optional
import torch
from torch import device
try:
import resource
except ImportError: # Windows does not provide the "resource" module
resource = None
SYSTEM = platform.sy... |
b814bbf7dbc7c7a45dbb19420a8a661fe7240dc13d7b6d41af40cea0cd6b6873 | Python | 3,840 | 154 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import glob
import numpy as np
from data_functions import load_data
from itertools import groupby
from operator import itemgetter
import matplotlib
matplotlib.use('Agg')
import pandas as pd
import matplotlib.pyplot as plt
from mpi4py import MPI
# us... |
17ed1e7fe86b3fc5745e7f48ef4b5476c9f3bbc614c89a4fdea2fe92a7d3d252 | Python | 3,843 | 121 | from torch import nn, Tensor
from typing import Optional, Union, Tuple
from utils.math_utils import make_divisible
from . import BaseModule
from ..misc.profiler import module_profile
from ..layers import ConvLayer
class InvertedResidual(BaseModule):
"""
This class implements the inverted residual block, as ... |
287afa622dc8dac0bec38d0b3384995ae09c8b4245e68ecf654a4c0fa888b889 | Python | 3,843 | 115 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
from logging import getLogger
import numpy as np
from tensorflow.python.keras.utils.data_utils import get_file
logger = getLogger(__name__)
def one_hot(labels, cl... |
5bda2a2e6c48b1d214fd92ee33c20a3bbb90da35ffd71f3ae631b309f5411291 | Python | 3,843 | 107 | import paddle.distributed as dist
import math
import paddle
import paddle.nn as nn
class _AllReduce(paddle.autograd.PyLayer):
@staticmethod
def forward(ctx, input):
input_list = [paddle.zeros_like(input) for k in range(dist.get_world_size())]
# Use allgather instead of allreduce since I don't ... |
a9e848c3dbb79a25db9736b84613a0822453697d1f05d0a262f7a49cda735fc8 | Python | 3,843 | 115 | """
DATA LOADERS
====================
This module is only a reorganization of Gabriel Guimaraes' original
implementation (http://github.com/gablg1/ORGAN). Carlos Outeiral has
only added documentation.
The code was initially borrowed from the SeqGAN code:
https://github.com/LantaoYu/SeqGAN
"""
import nump... |
63f36d3ffdff398bb92c80d6e7d1d3053f7346b15b9f1e399032a00e13320b5f | Python | 3,850 | 108 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
a16d434e9fbb5546877cc8e4924cbda54824687ac63e0a5906c9eaf3bcb65100 | Python | 3,850 | 100 | """Real tier: drive an actual LAMMPS binary with an exported MACE model.
Uses the ML-IAP unified path (`pair_style mliap unified`), which works with a
stock LAMMPS build that has the ML-IAP package and Python support — no MACE
plugin compilation required. The native `pair_style mace` route needs a
patched LAMMPS build... |
fc6a7aa67da5ee0f24cb04db35c302638b62b6066c6bc29d9c5b53bd2a595b6c | Python | 3,850 | 92 | import os
import torch
import hydra
from omegaconf import OmegaConf
from dig.xgraph.evaluation import XCollector
from dig.xgraph.utils.compatibility import compatible_state_dict
from benchmarks.xgraph.gnnNets import get_gnnNets
from benchmarks.xgraph.dataset import get_dataset, get_dataloader
from benchmarks.xgraph.Ra... |
40169d274856725efbe17218e74bac72796d9200d560923b39e81b6eac01df48 | Python | 3,851 | 119 | r"""Compute and visualize a geodesic regression on SE(2).
The generative model of the data is:
:math:`Z = Exp_{\beta_0}(\beta_1.X)` and :math:`Y = Exp_Z(\epsilon)`
where:
- :math:`Exp` denotes the Riemannian exponential,
- :math:`\beta_0` is called the intercept,
- :math:`\beta_1` is called the coefficient,
- :math:`\... |
83276d5bcdaa4aee33199bcb68d86013628dc8a42a185a69067dd13c5311e1e2 | Python | 3,855 | 145 | """Numpy based linear algebra backend."""
import numpy as _np
import scipy as _scipy
from numpy.linalg import (
cholesky,
det,
eig,
eigh,
eigvalsh,
inv,
matrix_power,
matrix_rank,
norm,
svd,
)
from scipy.linalg import expm
from ._common import atol
def _transpose(array):
... |
cf4597c10a45a655e57556170366f399aea369e7742887ad4b6e4fcc5c43973a | Python | 3,855 | 107 | from PymoNNto.Exploration.Network_UI.TabBase import *
class weight_tab(TabBase):
def __init__(self, title='Weights', weight_attrs=['W']):
super().__init__(title)
self.weight_attrs = weight_attrs
def add_recorder_variables(self, neuron_group, Network_UI):
return
def initialize(sel... |
aee4ffb2eb36c14a7af518090924160cec255baf5154e55e689e53f24f09350d | Python | 3,857 | 157 | import nest
import matplotlib.pyplot as plt
import numpy as np
import os
import time
from globparams import *
import random
from pynestml.codegeneration.nest_code_generator_utils import NESTCodeGeneratorUtils
#############################################################
# model generation
################... |
cba10c99f7dcc09219aadbc6964baa971c0eb127ba1d5282541bce278e4d6a5a | Python | 3,858 | 135 | #!/usr/bin/env python3
from __future__ import annotations
import argparse
import copy
import datetime
import hashlib
import json
import pathlib
from typing import Any, Dict, List, Sequence, Tuple
SHARD_KIND = "chroma-python-test-inventory-shard"
MERGED_KIND = "chroma-python-test-inventory"
def main() -> None:
... |
b707f2d1fc3ef10187c7d245b428d67b5f28352e0e2af275115653f172a26b43 | Python | 3,861 | 101 |
from sparse_ct.tool import plot_grid
from sparse_ct.data import image_to_sparse_sinogram, ellipses_to_sparse_sinogram
from sparse_ct.reconstructor_2d import (
IRadonReconstructor,
SartReconstructor,
SartTVReconstructor,
Sar... |
4371fe1254a460f07a098195efb0cc852d810a4c400a24f21609a84c595bd736 | Python | 3,862 | 124 | import pytest
import geomstats.backend as gs
import geomstats.datasets.utils as data_utils
from geomstats.geometry.discrete_surfaces import DiscreteSurfaces, L2SurfacesMetric
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test.test_case import pytorch_backend, torch_only
from geomstats.t... |
c2a26500f24ab1177ec9c37d870fabd38f9842494f0ef2c6517cb45eb532a2d9 | Python | 3,862 | 124 | """Matched molecular pairs"""
from __future__ import annotations
__all__ = ["Icolos"]
import os
import shlex
import json
import tempfile
import time
from typing import List, IO
import numpy as np
from pydantic.dataclasses import dataclass
from .component_results import ComponentResults
from .run_program import run... |
c572278698fe36f90556b3851ffe81d27f6e69eb7cbf4b99ffa3c315e4b7cc83 | Python | 3,863 | 94 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import os
import time
import argparse
from pathlib import Path
from subprocess import check_call
from concurrent.futures import ProcessPoolExecutor
from openfl.utilities.utils import rmtree
from tests.github.utils import create_collabor... |
eaa39a23b3dc5799c678aa474909c68798ecc52fb9b93960830c559b7db63919 | Python | 3,863 | 95 | """
Plot an excerpt of the input data and corresponding trigger times.
"""
import matplotlib.pyplot as plt
import seaborn as sns
import argparse
import os
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_int, none_or_float
from utils.neo_utils import time_slice
CLI = argparse.ArgumentPar... |
fbdfedf270a5e4785c1a2d189a36731de6685a6b3a7869d1a17d6081b69ca996 | Python | 3,864 | 92 | import os
from rdkit import Chem
from rdkit.Chem import rdChemReactions
import time
import pickle
from collections import defaultdict
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
def filter_duplicate_invalid(uspto_file=os.path.join("..", "data", "original_data", "data_from_USPTO_utf8"),
... |
5fc498e6e5d67019092fa50479c35ba1f072729e6b3bd5c7319e494ffc33d7c7 | Python | 3,866 | 121 | # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
4b78095c2208befd961e3b91ebbeb706442929862c9435ac39ad940a2ea959f7 | Python | 3,868 | 109 | import geomstats.backend as gs
from geomstats.geometry.spd_matrices import SPDMatrices
from geomstats.geometry.symmetric_matrices import SymmetricMatrices
from geomstats.test.data import TestData
rand = gs.random.rand
class AgainstNumpyTestData(TestData):
def _array_data(self):
func_name = "array"
... |
9128d42bea9cc7288523399da14752c71bca5bb640cde9d234b503b53d8bfd5e | Python | 3,869 | 103 | import gradio as gr
from .utils import load_ct_to_numpy, load_pred_volume_to_numpy
from .compute import run_model
from .convert import nifti_to_glb
class WebUI:
def __init__(self, class_name:str = None, cwd:str = None):
# global states
self.images = []
self.pred_images = []
... |
d173599117e521dd02fc49f976066015a94a3c209daf607f30dfbba685a7e6e6 | Python | 3,869 | 125 | from typing import List, Dict, Any, Optional, Union
import numpy as np
import pandas as pd
from chromadb.api.types import QueryResult, GetResult
def _transform_embeddings(
embeddings: Optional[List[np.ndarray]], # type: ignore
) -> Optional[Union[List[List[float]], List[np.ndarray]]]: # type: ignore
"""
... |
a099201e0520ebed52353b83d90571ac748126715091380e7e8e317a7a4cfabf | Python | 3,870 | 96 | """
Plot an excerpt of the input data and corresponding trigger times.
"""
import matplotlib.pyplot as plt
import seaborn as sns
import argparse
from pathlib import Path
import os
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_int, none_or_float
from utils.neo_utils import time_slice
C... |
838835e11e7c97e2e31c8b94ace29193904cf4c3e74a2ba5e88399efd7841e2e | Python | 3,875 | 77 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.Visualization.Reconstruct_Analyze_Label.Reconstruct_Analyze_Label import *
class sidebar_image_module(TabBase):
def add_recorder_variables(self, neuron_group, Network_UI):
return
def initialize(self, Network_UI):
... |
1a171abcc81096adc8cee1f0ca9c714b211c7b21da9ff8dd6ebaacf0dd95a018 | Python | 3,877 | 143 | """The video generator tool is used to generate videos from the tracking
data generated by the idtracker.ai software, see :ref:`video generator`."""
import argparse
import logging
from pathlib import Path
from idtrackerai import IdtrackeraiError, Session
from idtrackerai.utils import wrap_entrypoint
from .general_vi... |
4b5b889692ee6a6823458cd784223a20e57ec617c91144db189ad722d699d168 | Python | 3,878 | 114 | """Run a small stochastic Myokit current-step experiment and save it for SanPy.
See:
https://github.com/MichaelClerx/myokit/blob/main/examples/1-1-simulating-an-action-potential.ipynb
20260910
had to install:
brew install sundials
then check sundials with
uv run python -m myokit sundials
"""
import numpy as np
impo... |
bc7f094ce0bb8390f05f72ad6566fe89f5ce00351294f062b5bea3a135c7020e | Python | 3,879 | 102 | #!/usr/bin/env python
import pandas as pd
import numpy as np
import argparse
def parse_data(data, blacklist=None):
blacklist = blacklist or set()
tokens = data.split("; ")
data_dict = dict()
geom_id = None
epoch = None
for t in tokens:
key, value = t.split("=")
if key in blackli... |
3e34fdbc706749ac10f49d958664b55036d9a4028c2e8e76677233b922cd9d1e | Python | 3,881 | 134 | from typing import Optional
from urllib.parse import urlparse
import pytest
from hypothesis import given, strategies as st
from chromadb.api.fastapi import FastAPI
def hostname_strategy() -> st.SearchStrategy[str]:
label = st.text(
alphabet=st.characters(min_codepoint=97, max_codepoint=122),
min... |
eee1ba4c974aad819f46d86c98024fbddf52670aa4f050b649a7d651a7cd4a16 | Python | 3,883 | 109 | import unittest
import torch.utils.data as tud
from torch import Tensor
from reinvent.models.linkinvent.dataset.dataset import Dataset
from reinvent.models.linkinvent.model_vocabulary import ModelVocabulary
from reinvent.models.linkinvent.model_vocabulary.vocabulary import (
SMILESTokenizer,
create_vocabulary... |
e9903c35898c323719e5385b915bd345fb9bf390432ed7260d7c59fcaee772f6 | Python | 3,884 | 95 | """
Plot an excerpt of the input data and corresponding trigger times.
"""
import matplotlib.pyplot as plt
import seaborn as sns
import argparse
import os
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_int, none_or_float
from utils.neo_utils import time_slice
CLI = argparse.ArgumentPar... |
6305104c530bd437da663cfab06671974273965b7f45aeb3bab5dc9e119934cf | Python | 3,885 | 119 | from live2p.start_live2p import start_live2p
### ----- THINGS YOU HAVE TO CHANGE! ----- ###
# Set these first to match makeMasks3D!!!
# I recommend using removing 110 pixels from each side. Maybe 120 for holography. Maybe less for vis stim. But
# it has to match whatever you did in MakeMasks3D.
# also set the max num... |
a76f1884814fe03bb97b0526fd93a48b3cbbe1f8c5749258bdabec475b94ed26 | Python | 3,886 | 133 | from geomstats.test.data import TestData
from .fiber_bundle import FiberBundleTestData
from .nfold_manifold import NFoldManifoldTestData
from .pullback_metric import PullbackDiffeoMetricTestData
from .quotient_metric import QuotientMetricTestData
from .riemannian_metric import RiemannianMetricTestData
class Discrete... |
1c11543a91f943c200dc56c88fdcaa62fa8dfa41ebca795f746885161ca5d391 | Python | 3,887 | 121 | """Core parametrizer classes for Stratified Spaces."""
import pytest
import geomstats.backend as gs
from geomstats.test.random import get_random_times
from geomstats.test.test_case import TestCase
from geomstats.test_cases.geometry.mixins import (
DistTestCaseMixins,
GeodesicBVPTestCaseMixins,
)
class Rando... |
d585711274c99517788e7fcb26f6a25da2244f7fc8ab2128d8b29f3dadd033d1 | Python | 3,889 | 129 | from __future__ import annotations
import itertools as it
import json
import operator as op
import textwrap
from math import ceil, floor, inf
from typing import Sequence
import more_itertools as itx
from snakebids.types import ZipList
def quote_wrap(val: str) -> str:
"""Wrap string in quotes, with additional c... |
2b89a386dc0d3ff92f38d68ff72ba05a3f4d78b857f87bdb829e2c9515a3690b | Python | 3,890 | 136 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# FileName: main
# CreatedDate: 2017-11-20 14:05:59
#
import argparse
import os
from datetime import datetime
import matplotlib.pyplot as plt
import pandas as pd
def main():
# setting option
parser = argparse.ArgumentParser(
description="draw graph f... |
946ea41cadfe982ccbab0569da995c5a542af2cf4871e23f984adb4c6d7b4adf | Python | 3,890 | 96 | """
Plot an excerpt of the input data and corresponding trigger times.
"""
import matplotlib.pyplot as plt
import seaborn as sns
import argparse
from pathlib import Path
import os
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_int, none_or_float
from utils.neo_utils import time_slice
C... |
8a71966f9620566c6e68340544237574a5f0fc67b943d7fd383c99021e27448e | Python | 3,891 | 97 | import argparse
import onnx
import onnx_graphsurgeon as gs
import numpy as np
from pathlib import Path
from paddle2onnx.legacy.command import program2onnx
from collections import OrderedDict
def main(opt):
model_dir = Path(opt.model_dir)
save_file = Path(opt.save_file)
assert model_dir.exists() and model... |
97f8d15fb7c019100ba61dc85ae2b0a5be93938ca0cda38a71937dc2df480d4f | Python | 3,892 | 122 | import logging
import time
from pathlib import Path
import scipy.io as sio
from live2p.offline import run_plane_offline_multifolder
from live2p.utils import tic, ptoc
# logging setup
# change for more or less information...
caiman_loglevel = logging.INFO
live2p_loglevel = logging.DEBUG
# changes how logs/updates ar... |
3daa99b9dfc762566b663f2e67c6f1b86583d4c12d971de056a74c9d7459563f | Python | 3,896 | 79 | import argparse
from .ConvNet import load_model
from .seqsharp_fcts import handle_args, load_data, validate, model_test, train, \
model_figures
from .train_eval import print_model_performance
def main():
sep_line = '-------------------------------------------------------' \
'---------'
# ... |
95b80521f7db1369f2e9fa3c708972104fc663d3bc751d3db95f8fda69a8d2d9 | Python | 3,899 | 134 | import argparse
import os
import torch
from src.dataset import build_datasets_from_cv_folds, get_dataloader
from src.models import ModelWrapper
from src.setup import setup
from src.trainer import Trainer
def parse_args():
parser = argparse.ArgumentParser("arguments for training")
# Model selection
pars... |
cc90a3b0d8c07910a74c6ea1d6e51d275c277aac0943b3733f0f6a5ec66a9372 | Python | 3,902 | 136 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# FileName: main
# CreatedDate: 2017-11-20 14:05:59
#
import argparse
import os
from datetime import datetime
import matplotlib.pyplot as plt
import pandas as pd
def main():
# setting option
parser = argparse.ArgumentParser(
description="draw graph f... |
d62b1f43c09ca912deecd0af2313eea0eef489a18082188e5bd51c6c12691d06 | Python | 3,904 | 156 | """
Django settings for WebLabelling project.
Generated by 'django-admin startproject' using Django 2.1.
For more information on this file, see
https://docs.djangoproject.com/en/2.1/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/2.1/ref/settings/
"""
# Author: ... |
677bbe7719a1da9b36f0c61a85c5322ada0c30a7c9d6752d105713b4dff0def7 | Python | 3,906 | 98 | """Regeneration targets: one module per family of goldens.
``regenerate.py`` does not know what can be regenerated. It asks this package,
which discovers every module beside this one and reads four names off it:
``ORDER``
an integer. ``--target all`` runs the targets in ascending order, ties
broken by name, b... |
f135af88156c586ea5cc4075611e3c1445d9b718407aad545fe289ef2bf49dea | Python | 3,906 | 100 | #### make_image_from_bin_renum.py
# Copyright (C) 2010 R. Cameron Craddock (cameron.craddock@gmail.com)
#
# This script is a part of the pyClusterROI python toolbox for the spatially
# constrained clustering of fMRI data. It converts a NPY file generated by
# binfile_parcellation.py, group_binfile_parcellation.py, or
#... |
e56a4c700958a7101cccfcb7b09aa6b5d403e6551e6a7a9b728f9e1d566d5b6d | Python | 3,908 | 110 | """Model output visualization — ROC curves and the cross-validated decoding figures.
Every function here takes arrays, not a result table: `BrainData.predict` returns a
`PredictResult` record plus the row-aligned out-of-fold decision values that go with it,
and these draw from those directly.
"""
import matplotlib.py... |
a251c28b08ece3065c890e5c392b85f480e66c136e7396d22d0a1e2df500f1c7 | Python | 3,911 | 82 | import io
import click
import pandas as pd
from uniprotparser.betaparser import UniprotSequence, UniprotParser
from curtainutils.common import read_fasta
import re
reg_positon_residue = re.compile("_(\w)(\d+)")
def lambda_function_for_msfragger_ptm_single_site(row: pd.Series, index_col: str, peptide_col: str, fasta... |
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