sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
82b2dbee69ae0466ab77f0ef6c2a061d0e79fdf7cd82d388762a697c5786c72b | Python | 9,374 | 273 | import numpy as np
import pandas as pd
from scipy import signal, ndimage, interpolate, stats
from scipy.interpolate import CubicSpline
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
from matplotlib.ticker import FormatStrFormatter
import warnings
import seaborn as sns
from pathlib impor... |
e06943de6c03f79d41640166f0e41f7fc11b566e90764c2b5c46022be298d802 | Python | 9,380 | 304 | # 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
#
# Unless required by appli... |
f9182c585d19d857a28c17d16f02dc928ef13bc07db5558789a79485fc454d8c | Python | 9,393 | 266 | # Copyright (c) 2021-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.
import logging
import math
from ty... |
af77d9f79bcdc49238ad4ba62b65274f571ba1c8ee128662836dd9fd013d4913 | Python | 9,402 | 238 | # Copyright (c) 2023 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... |
a4faa235192a6f30214fa85e4ad31a6af5807bd2a7c291375aa0bf143113ef7b | Python | 9,404 | 231 | # 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
#
# Un... |
dbdfa0b956c0d7bd253979ba38159dbb14ab6afa637a4c08026d8fc3390aa758 | Python | 9,409 | 249 | """
data loader for adaptive sampling based on binary maps.
compare randomly cropped image to corresponding binary map area.
I. pseudo code
A. initialize
i. grap image crop/binary map
ii. calculate total binary area w/in crop (sum)
B. iterate
i. while (binary map < 50%):
a. ... |
95294c50620c590085329c84f463d6ac320969083da22ea7cc3c45b387c1175d | Python | 9,412 | 283 | # -*- coding: utf-8 -*-
"""
Provides the abstract :class:`Measure` base class and some popular measures.
Measure instances are identified by a unique :attr:`~Measure.short_name`, which
is used by the :mod:`~dival.evaluation` module.
"""
from abc import ABC, abstractmethod
from warnings import warn
import numpy as np
t... |
c06dffaadeacda6abd342eb13ae01ff7d3032c2700b67289c497114d6eb8961b | Python | 9,417 | 260 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.runtime package FederatedRuntime class."""
from __future__ import annotations
import logging
import os
import sys
from datetime import datetime
from pathlib import Path
from typing import Any, Dict, List, O... |
2277bd0cb76a5bbdb12e7a0780f9e92a348d0a45d2657e043b89f218963ebb42 | Python | 9,425 | 292 | # Copyright (c) 2019 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... |
f32ce944e961633f9f9a037cd80559b338b14d98195d2c0a3bf7c7ff8e966c47 | Python | 9,430 | 273 | import logging
from chromadb.db.impl.sqlite_pool import Connection, LockPool, PerThreadPool, Pool
from chromadb.db.migrations import MigratableDB, Migration
from chromadb.config import System, Settings
import chromadb.db.base as base
from chromadb.db.mixins.embeddings_queue import SqlEmbeddingsQueue
from chromadb.db.mi... |
59880504bc75b62ade7656a793b74a54e9e0f0676dabeebb0c13e906ca89f96b | Python | 9,432 | 256 | from time import sleep
from chromadb.api import ClientAPI
from chromadb.api.types import IndexingStatus
from chromadb.test.conftest import skip_if_not_cluster
from chromadb.test.utils.wait_for_version_increase import (
get_collection_version,
wait_for_version_increase,
)
@skip_if_not_cluster()
def test_index... |
e3173bec41923b90854181799c7d11cdcbad57ca3aa1cfec2e461be3f459fbd0 | Python | 9,435 | 271 | import logging
import multiprocessing
import shutil
import sys
from argparse import ArgumentError
from importlib.metadata import version
from importlib.resources import files
from pathlib import Path
from typing import Any
from idtrackerai import IdtrackeraiError, Session, conf
from idtrackerai.utils import (
LOGG... |
5c7ed8645fe5ef9d442b4586e36ae82464bef3d8cf62faf740e2f2efe1779011 | Python | 9,439 | 230 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from lightning.pytorch.utilities.seed import isolate_rng
from nequip.nn.graph_model import GraphModel
from nequip.nn.compile import CompileGraphModel
from nequip.utils import (
dtype_f... |
9712643ac27cdfc847cb8acd19ede2c9c33f40bf27dfa21784116663f513f31a | Python | 9,448 | 279 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Components Timeout Configuration Module"""
import asyncio
import logging
import os
import time
from contextlib import contextmanager
from functools import wraps
from threading import Thread
logger = logging.getLogger(__name__)
class ... |
11d236e4cb0f7461c4a68af1ac1f38a9ca08f5ce4cb8a35b378591e28a4c1060 | Python | 9,450 | 232 | # Copyright (c) 2024 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... |
9485fef4c2118263a94035d4066ab31a6d2373c859bd63280708cac9791ddbe0 | Python | 9,457 | 272 | """Utility functions for managing collection statistics.
This module provides standalone functions for enabling, disabling, and retrieving
statistics for ChromaDB collections. These functions work with the attached function
system to automatically compute metadata value frequencies.
Example:
>>> from chromadb.uti... |
3247972a71a3b4df42a4daea2e15b254af68a35e8d84a376637d16a7e72ad957 | Python | 9,458 | 264 | # -*- 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... |
e2ce05c71a0cf1a60374cc9794eccbbd08d4bb2d3f2e9a6166ede9bfa3472307 | Python | 9,463 | 311 | import torch
import numpy as np
torch.set_printoptions(precision=9)
if torch.cuda.is_available():
device = "cuda"
else:
device = "cpu"
def test_PosNet():
from mlspm.models import PosNet
cnn = PosNet(
encode_block_channels=[4, 8, 16, 32],
encode_block_depth=2,
decode_block_ch... |
6c62d1065565c07f895760b96f3f67cf7b5c309c1bc835a71b22cb758ac3098b | Python | 9,465 | 233 | import pytest
import numpy as np
from nltools.data.designmatrix import DesignMatrix
class TestDownsampleNonIntegerRatio:
"""F083: non-integer sampling ratios must not produce an oversized final group."""
def test_non_integer_ratio_no_oversized_final_group(self):
"""2 Hz -> 0.7 Hz (ratio ~2.857) must ... |
8b753b07b13ec02c04b4bf4fdee8784d95a733a7c6d6f200349b3c725d0d9e59 | Python | 9,479 | 260 | """Lazy fetcher for files hosted in the `nltools/niftis` HF dataset.
Covers MNI templates, parcellation label maps, the parcel-names CSV, and
any other resources living under huggingface.co/datasets/nltools/niftis.
First call for a given file downloads it into the local HF cache
(`~/.cache/huggingface/hub` by default)... |
a708a3ebd6977d13966f292233cb235fea51680c2a3b4a7863e73572c80e0b4e | Python | 9,481 | 270 | import torch
import os
import numpy as np
import pandas as pd
import pytorch_lightning as pl
from lightning.pytorch.utilities.combined_loader import CombinedLoader
from rdkit import Chem
from torch.utils.data import Dataset as TorchDataset
from torch_geometric.data import Data as GeometricData
from torch_geometric.loa... |
3da4c8d030fc096ea6354bed5b6f222cc4a8d5b164a6b754ddd9dd98faef8099 | Python | 9,483 | 242 | # Copyright (c) 2023 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... |
66cee0629421326cd2f0ed03d25555b4a00a22a28a9408956620c59fde88a921 | Python | 9,492 | 295 | # 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 app... |
9a34b6de813a6a5393f220205d753dd2bae9b53adc36aefdaba11799944d22bf | Python | 9,493 | 262 | import math
from typing import Iterable
import numpy as np
import torch
from model_angelo.utils.misc_utils import assertion_check
from model_angelo.utils.residue_constants import (
restype_1_order_to_hmm,
index_to_hmm_restype_1,
num_prot,
restype_1_to_index,
restype_3_to_index,
)
from pyhmmer.pla... |
e3a258071fb826ab3b2c2956e2556d629726f47ce0c8a876fe261486a2e236fe | Python | 9,493 | 231 | """
Algorithm:
- leave one row (seed) out
- run ppca on remaining data
- apply the extracted dimensions to each set of left-out ratings for each country,
resulting in component scores for each country and seed image
- to compute significance, loop through each pair of countries
- correlate their component scores and ... |
a7009d23fd7db3c15e6f4c5c84d40f91b42395c14bd477590c5f8d3c0f2817fb | Python | 9,496 | 253 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.interface.participants module."""
from typing import Any, Callable, Dict, Optional
class Participant:
"""Class for a participant.
Attributes:
private_attributes (dict): The private attribu... |
797efe377e0c4e9835e01499e64894c82febfc629c84d5f0c8ce2580a693f458 | Python | 9,500 | 291 | # Reference: https://xylambda.github.io/blog/python/pytorch/machine-learning/2021/01/04/pytorch_trainer.html
import time
import numpy as np
import pandas as pd
import torch
import torch.nn.functional as F
from sklearn import metrics
from tqdm import tqdm
class Trainer:
"""
Parameters
----------
mode... |
0ae818cc3e64475d3da037439f77ac0db45c51487705599f8df9c8750c131172 | Python | 9,502 | 247 | import PySpin
from video_stream import ImageSource
import time
class FLIRImageSource(ImageSource):
default_params = {
**ImageSource.default_params,
"exposure": 8000,
"trigger": True,
"frame_rate": None,
"stream_id": 0,
"acquisition_timeout": 5000,
"pyspin": ... |
1be87ca548ca92b89f093b62e232260858ac23c7ad4ae7d0a8aac36092d138c0 | Python | 9,503 | 290 | # copyright (c) 2021 PaddlePaddle Authors. All Rights Reserve.
#
# 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 applica... |
0a09657930d486ca653fad9b4ed520969d83190c85002d7c3acca7aaf1536ad7 | Python | 9,504 | 321 | """Class for the spider.
Lead authors: Anna Calissano & Jonas Lueg
"""
import geomstats.backend as gs
from geomstats.geometry.euclidean import Euclidean
from geomstats.metric_geometry.point_set import (
Point,
PointBatch,
PointSet,
PointSetMetric,
)
from geomstats.metric_geometry.vectorization import ... |
b99d40a170debe33995959339887e707ec55f18976c5a0b809eb6ca6bf6212e3 | Python | 9,509 | 210 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from lightning.pytorch import seed_everything
import e3nn
from .global_dtype import _GLOBAL_DTYPE
from .versions.torch_versions import (
_TORCH_GE_2_6,
_TORCH_GE_2_9,
_TORCH_... |
cbbd7fe89f2d60ed34c9120f1bd138df66bf417e1e67ed66eaad050a3a6160b5 | Python | 9,512 | 330 | import numpy as np
# import matplotlib.pyplot as plt
import torch
import h5py
import torch.nn as nn
from torch.utils import data
import itertools
# number of available gpu
ngpu = 1
batch_size = 16
###################################################
## Loading the data
dataRoot = "../../data"
labelFiles = "labels-... |
cda4214857f9f54dc05eb0dd88fae501c62d21e9bfa7609c1b06f1af7c95dee2 | Python | 9,513 | 250 | #!/usr/bin/python3
import os, sys
import argparse, serial, threading
import datetime,time
## Input Parameters
parser = argparse.ArgumentParser()
parser.add_argument("Experimenter_ID", help="Please indicate the experimenters ID")
parser.add_argument("Subject_ID", help="Please the Subject's ID")
parser.add_argument("Ex... |
1ef4d48a4986973ed31e935de3cbf185d6280fcb6551316469452a6f1648bab4 | Python | 9,517 | 323 |
import numpy as np
from sleepy.gui.tagging.model import DataSource
class Dataset:
def load(path):
"""Static API-method that returns a raw data object for a given path.
Must be implemented by direct subclasses.
:param path: An absolute path to a file whose contents should be loa... |
656c59471654b4b94e6852b0cc022cda3bbd352216fd5d3144ab7dc2d1ed1d06 | Python | 9,518 | 323 |
import numpy as np
from sleepy.gui.tagging.model import DataSource
class Dataset:
def load(path):
"""Static API-method that returns a raw data object for a given path.
Must be implemented by direct subclasses.
:param path: An absolute path to a file whose contents should be loa... |
f57dd8b5f16128b6897101cfb64c089d4ce4098fac82bcd4caecfff076da02fe | Python | 9,525 | 232 |
# -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models 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 Cognitiv... |
e3c48c73d3783f84e8bdebe1b176dac82821794119f9623b7e8a6bc4f5cffac8 | Python | 9,527 | 216 | # -*- coding: utf-8 -*-
"""
Helper file cotaining custom functions
Clean code for publication
@author: Sebastian Molina-Obando
"""
#%%
#Importing packages
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.stats import pearsonr, levene
from itertools import combinations... |
e1190d8d233adc4488c2f51238a758b883e9064fd891f23f8e9ae77fcc2ddcf2 | Python | 9,533 | 243 | """Build and filter per-spike waveform clips for one SanPy analysis."""
from __future__ import annotations
from typing import TYPE_CHECKING, Any
import numpy as np
from sanpy.sanpyLogger import get_logger
if TYPE_CHECKING:
from sanpy.bAnalysis_ import bAnalysis
logger = get_logger(__name__)
class SpikeClips... |
945d9173b85cddf4e752a57dc6ef49e61bc3e59d0d9cefdc86aa89956e3271fd | Python | 9,534 | 311 | # 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
#
# Unless required by appli... |
214b3297b8d3a62dc01df15b57cee7c02801019174a50e66a3249ce50943d6e2 | Python | 9,540 | 299 |
from sleepy.test.core import TestBase
from sleepy.gui.processing.core import Preprocessing
from sleepy.gui.processing.supported import SUPPORTED_DATASETS
from sleepy.processing.dataset import Dataset
import unittest
from unittest.mock import MagicMock, patch
import numpy as np
class MockingDataset(Dataset)... |
295afeb6e5c442c8251c8e9633a75de5ceb7df334113946a7884c759f3477016 | Python | 9,546 | 283 | """
Utils for featurizing a small molecule (amino acid residue) from their structures.
"""
import dgl
from typing import Union, List
from transformers import T5Tokenizer, T5EncoderModel
import torch
import torch.nn as nn
import numpy as np
from dgllife.utils import (
mol_to_bigraph,
PretrainAtomFeaturizer,
... |
0cbab5eb36eb844c6dce812df5a3916b313918d54303caf99317c1daaf1bce5d | Python | 9,547 | 266 | """Prototype for the new heart of the scoring component
A scoring function is composed of components. An aggregation function
combines components into the final scoring function. Each component has a
weight and cna be transformed from a function. Components report a primary
score for training and possibly secondary... |
6472217a67dab6131ea3e95a870517e391d011341784572d0182256c6dba3dc3 | Python | 9,555 | 263 | import numpy as np
import glob
import pickle
from umap.parametric_umap import ParametricUMAP
import tensorflow as tf
#tf.compat.v1.disable_eager_execution()
sess = tf.compat.v1.Session()
tf.compat.v1.keras.backend.set_session(sess)
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Lambda,... |
8c15783ad261cb35b8a747b40dea7ebafa5255a01341e6ab1cbeed5c3ec06e14 | Python | 9,557 | 183 | # %%
import os
import numpy as np
import time
import h5py
import sys
from scipy import sparse
from scipy.io import savemat, loadmat
import multiprocessing as mp
sys.path.insert(1, '../..') # the path containing "suns" folder
os.environ['KERAS_BACKEND'] = 'tensorflow'
# os.environ['CUDA_VISIBLE_DEVICES'] = '0' # Set w... |
9203604ca89c4ce2295971831ca03da15bd5a614b2c944ecd7768dfb1b39deec | Python | 9,563 | 161 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... |
bafe00b85b988ad083ea57710fa675bfb12b4e949d0e4a6173834ac117bb019c | Python | 9,566 | 181 | import os
import requests
import numpy as np
from Humatch.utils import (
get_ordered_AA_one_letter_codes,
get_CDR_loop_indices,
get_indices_of_selected_imgt_positions_in_canonical_numbering
)
# gl arrays added to compiled env package_data
HUMATCH_CODE_DIR = os.path.dirname(os.path.abspath(__file__))
GL... |
f8130aa5c9365de3c1e01dd46c3f48c72d98fb145c12f99c0d914aab4b5b30b3 | Python | 9,573 | 303 | import os
import numpy as np
import pandas as pd
import json
import torch
from torch_geometric.data import HeteroData
import torch_geometric.transforms as T
from sklearn.metrics import roc_auc_score, average_precision_score
from GeNNius import Model, EarlyStopper, shuffle_label_data
def train(train_data):
mode... |
f5435eebfc7d6e24fa1fd5fe156c061292e8381e7e9934624a1df72b2e2e2c5f | Python | 9,579 | 166 | from DeepPurpose import utils, dataset
from DeepPurpose import DTI as models
import warnings
import itertools
import numpy as np
import pandas as pd
import wandb
from tqdm import tqdm
import sys
warnings.filterwarnings("ignore")
import random
import argparse
def main(num_samples, val_setting, cuda_id, num_workers, da... |
470b87b977d432a00e710689ba66e1866e386586942f0bec16c93e83f58e6104 | Python | 9,580 | 250 |
from sparse_ct.tool import plot_grid
from sparse_ct.data import image_to_sparse_sinogram
from sparse_ct.reconstructor_2d import (
IRadonReconstructor,
SartReconstructor,
SartTVReconstructor,
DgrReconstructor,
SartBM3DReconstructor)
import logging
logging.basicConfig(
filename='dgr_example_32_... |
9ba7a4ad30e5c58c050277eacbe03708ef83f8fa447b25a48f149d86dd5f10ab | Python | 9,583 | 234 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.Visualization.Visualization_Helper import *
class criticality_tab(TabBase):
def __init__(self, title='Criticality', param='output', mask_param='Input_Mask', timesteps=500, mask_color_add=(-100, -100, -100)):
super().__init__(t... |
f845acfd141038e40d17aac7e1b836604881343a75b47699ed34a64afe886624 | Python | 9,585 | 122 | # -*- coding: utf-8 -*-
import functions.rate_coding
import numpy as np
import functions.manifold
import functions.Graphs
import matplotlib.pyplot as plt
import functions.statistics_test as st
from scipy import stats
#%% Load data
data = np.load('/datapath/dataset.npy', allow_pickle=True).item()
#%% 3B ... |
5dcc0285e4f93412506db9c264596b75139331836bf25e3b66e20a70f38e9e86 | Python | 9,586 | 299 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 05.12.2023
# Author: Hermann Romanek
# Maintainer: Hermann Romanek
# Contact: sniffles@romanek.at
#
import logging
import os
from sniffles.config import SnifflesConfig
from sniffles.snf impo... |
9f65f0f6f16b2a965a2aed38a4e98f61c5437e3cbb9ca9fb4997648c908ce537 | Python | 9,599 | 223 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by finding local minima preceding a prominent peak in the channel signals.
"""
import neo
import numpy as np
import quantities as pq
from scipy.signal import find_peaks
import argparse
from pathlib import Path
from utils.io_utils import load_n... |
954da97c7d31e29bd05c53f3f137fcb4e4ceca67adb908f03df07d17a76a609a | Python | 9,601 | 196 | """The junction-anchor check: what it flags, and what it refuses to call a defect.
It proposes no repair. That is `arda.cdr3fix`'s job and it does it (#711); this classifies the
**submitted** sequence, which is what a chunk edit would change.
"""
from __future__ import annotations
import polars as pl
import pytest
f... |
69be2cec6001b51dcda1910932a3410bd237d66b3cc7ea857459222696112193 | Python | 9,603 | 223 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by finding local minima preceding a prominent peak in the channel signals.
"""
import neo
import numpy as np
import quantities as pq
from scipy.signal import find_peaks
import argparse
from pathlib import Path
from utils.io_utils import load_... |
a93c3375523e0e94e79100827634b17e3b3241a6cc368c8bf7c08a458c612125 | Python | 9,605 | 271 | """
Functions for removal of neuropil from calcium signals.
Authors:
- Sander W Keemink (swkeemink@scimail.eu)
- Scott C Lowe
Created:
2015-05-15
"""
import numpy as np
import numpy.random as rand
import scipy.signal as signal
from sklearn.decomposition import FastICA, NMF, PCA
def separate(
S, ... |
1bf8dcbf5003ac814580a3e1ce55917ed2324fe3b97c39814ce6a5c2483fe30d | Python | 9,606 | 248 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.utilities package."""
import inspect
import itertools
from types import MethodType
import numpy as np
from openfl.experimental.workflow.utilities import ResourcesAllocationError
def parse_attrs(ctx, excl... |
29b9ce1fe98b15a37c0cfcc61b33e80c5aa4495ce0e44cf0a4e91b0e639449ab | Python | 9,607 | 268 | import time
import h5py
import json
import sys
import os
import six
import copy
import argparse
import torch
import torchfields
import numpy as np
from pathlib import Path
from tqdm import tqdm
from cloudvolume import CloudVolume
def get_dset_path(dst_folder,
x_offset,
y_offset,
... |
5de19ad2e8f3c83220c87845d216e99f243f35cff180809bd96b854ea8cdd6e6 | Python | 9,614 | 281 | from dataclasses import dataclass, field
from typing import List, Dict, Any, Union, Set, Optional
from chromadb.execution.expression.operator import (
KNN,
Filter,
GroupBy,
Limit,
Projection,
Scan,
Rank,
Select,
Where,
Key,
)
@dataclass
class CountPlan:
scan: Scan
@datac... |
3cd5cf6393f275f5f1f44fe781670e9c9de6bed85f7b945dfa14dba19aaaebfe | Python | 9,618 | 279 | # ==============================================================================
# Copyright 2025 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import os
from p... |
dc389a1381145a4ce1699cf218d4d5deba271ff52ab21b502b99901b4c07efa1 | Python | 9,618 | 264 | # Based on the code from: https://github.com/klicperajo/dimenet,
# https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/nn/models/dimenet_utils.py
import numpy as np
from scipy.optimize import brentq
from scipy import special as sp
import torch
from math import pi as PI
import sympy as sy... |
2f2d693d16d3846be8016cd1a0b9876bbf0fa9aaabc0c5f9e6dc227e70d0e388 | Python | 9,627 | 315 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import torch
from torch.nn import CrossEntropyLoss, KLDivLoss, NLLLoss, SmoothL1Loss, BCELoss, BCEWithLogitsLoss
import torch
from torch import nn
import torch.optim as optim
from torch.optim.lr_scheduler import ReduceLROnPlateau
import torch.utils.dat... |
1c2da9617624b97c636fe987471a9c883f179a49e4250f4c51b46e204de91a76 | Python | 9,630 | 276 | import sys
from typing import Sequence
from typing_extensions import TypedDict, NotRequired
from importlib_resources.abc import Traversable
import re
import hashlib
from chromadb.db.base import SqlDB, Cursor
from abc import abstractmethod
from chromadb.config import System, Settings
from chromadb.telemetry.opentelemetr... |
8170fc8735ddb6bb7750a6e3e4adc6bbc0b5fb2aed158ad12517004280eac6a3 | Python | 9,631 | 262 | import argparse
import glob
import importlib
import os
import numpy as np
import shutil
import sklearn.metrics as skmetrics
import tensorflow as tf
from data import load_data, get_subject_files
from model import TinySleepNet
from minibatching import (iterate_minibatches,
iterate_batch_seq_min... |
6f88fb25bd8a944ce3542cdd8ef45f21aa07dc2e0bf685300d02d78df3f1de61 | Python | 9,642 | 274 | from PymoNNto.NetworkCore.Base_Tagable_Object import *
import numpy as np
from numpy.random import *
from numpy import *
from functools import wraps
import builtins
bool = builtins.bool
def lognormal_real_mean(mean=1.0, sigma=1.0, size=1):
mu = -np.power(sigma, 2) + np.log(mean)
return lognormal(mu, sigma, si... |
7c250279e08c69c78c7df9e61867b39d896b9e58f2d2c112f698f16e83674981 | Python | 9,642 | 283 |
"""
See:
https://github.com/easy-electrophysiology/load-heka-python
And the older code
https://github.com/campagnola/heka_reader
I clones and pip install -e
Needed to comment this out in load_heka_python/readers/data_reader.py
in def run_checks()
# abb 2023
# assert not data_kind["IsLeak"],... |
2628afbef95bcc5e6d5cc159f7089a06b7ed15ea86e7b07399cfbe821ebee489 | Python | 9,647 | 245 |
import random
import matplotlib.pyplot as plt
import numpy as np
import os
from skimage.color import rgb2gray, gray2rgb
from skimage.metrics import (
mean_squared_error,
structural_similarity,
peak_signal_noise_ratio
)
from skimage.transform import iradon, iradon_sart
import torch
from torchvision impo... |
bea8beb3763c1def9f34ccdb328bdea43b994a1455346f52d51a97fa80a29a42 | Python | 9,647 | 253 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.model_selection import train_test_split
from sklearn.linear_model import RidgeClassifier
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import C... |
533c68b071dc9bcfdb5702d393b83cb6682a12c0c19ff81d05cece7b0b949b78 | Python | 9,652 | 250 | # 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
#
# Un... |
51b95dcd9a50353f9e2e9d9f0523a8f97455f8d4ab069d8a4615102e405bb81a | Python | 9,661 | 267 | # Based on the code from: https://github.com/klicperajo/dimenet,
# https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/nn/models/dimenet_utils.py
import numpy as np
from scipy.optimize import brentq
from scipy import special as sp
import torch
from math import sqrt, pi as PI
try:
im... |
678c17e139f8f1e7358d424d2ddeda3bc3a7056a7dd6c8a6ed7bca629986d281 | Python | 9,663 | 236 | """How the ``MACELES`` anchor is driven, for both of its goldens.
Shared by ``tests/golden/regenerate.py`` and ``tests/golden/test_tiny_maceles.py``
so that the reference and the assertion cannot drift into evaluating two
slightly different things -- the failure mode that makes a golden either
mysterious or, worse, va... |
7107cbdba646b4493a003cac9a1e208b5a7a59834e62a2c39ce6b2114d5bd305 | Python | 9,673 | 287 | """
Train a baseline autoregressive model that uses a causal LM approach to generating
series of angles
"""
import os
from pathlib import Path
import json
import argparse
from datetime import datetime
import logging
import multiprocessing
from typing import *
import numpy as np
import torch
from torch.utils.data impor... |
76be06716c05436426b5936ec6a6a6400112ed48897c28270332b7f2fec7663e | Python | 9,673 | 254 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2019 Shigeki Karita
# Apache 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
"""Multi-Head Attention layer definition."""
import math
import torch
from torch import nn
from fairseq.modules.rotary_positional_embedding import (
RotaryPositionalEmbedding... |
0c8766a4ca1a2bd317204f487a02f59b150c1b6f3694e2fc55bbbe8008dcaa01 | Python | 9,679 | 266 | r"""
Large-Scale Networks with PopulationTemplate and Connectivity
=============================================================
Building large networks of coupled neural populations is a core workflow in computational
neuroscience. With the *legacy* PyRates API, a network of :math:`N` all-to-all coupled
nodes require... |
c28384a64edcc63e4155d6215593fd1757dc089396cd90331e04b9197472b50c | Python | 9,683 | 230 | # 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
#
# Unless required by appli... |
3f6f1657aaa44b6d991a5390f482b587cdb984c78138b02259c5021f074ec74c | Python | 9,692 | 185 | import math
import numpy as np
import time
from scipy import special
import h5py
import fissa
import os
from scipy.io import loadmat
def generate_masks(network_input:np.array, file_mask:str, list_thred_ratio:list, dir_save:str, Exp_ID:str):
'''Generate temporal masks showing active neurons for each SNR frame in "... |
f6d628792f085a217aa562480ad4d156e9be4f02f78e9490614fe656f31bdabc | Python | 9,693 | 179 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
'''
-NEW BRANCH CREATED FROM P1NAN_ASTRO_CORE_SLIMv0_local.py
made for main run file v5_2 with astrocyte bias optimization
DIRECT COPY OF P1NAN_ASTRO_CORE_SLIMv1_local.py
- HERE FIXED MODEL OF ASTROCYTE W... |
f4ff1ba65d2e6191178309632ca40d707ec5cd558d8f87cf18c81511b793e2b4 | Python | 9,695 | 277 | """The six `MACE_*` variables the ML-IAP coupling reads.
`MACELammpsConfig.__init__` is the only place they are read, and nothing
exercised any of them. They are the knobs a user reaches for when a LAMMPS run is
slow or on the wrong device, which is the worst time to discover that one of them
is spelled differently th... |
36a1a7076b6471341053cd3c6fc3c0342b4a39bc42ea8831cb58b807372301c8 | Python | 9,696 | 231 | import argparse
import json
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from sklearn.decomposition import PCA
from sklearn.metrics import silhouette_score
from pydfc.ml_utils import (
LE_transform,
PLSEmbedder,
dFC_feature_extraction,
find_available_subjects,
... |
c7fae8f9fc1e1cdd67b7ce5060c3663645c29221e465f6196a13208248f2c2d5 | Python | 9,713 | 236 | import os.path as osp
import h5py
import numpy as np
import warnings
from tqdm import tqdm
import torch
import torch.nn.functional as F
from torch_geometric.data import Data
from torch_geometric.data import InMemoryDataset
class FOLDdataset(InMemoryDataset):
def __init__(self,
root,
... |
fe5d269e51f1f901e4976ea2fbbd8c2c0a0cce31160559ea0eb60c95ea48ca67 | Python | 9,713 | 257 | """Train the ``ScaleShiftMACE`` parity anchor.
Unlike its plain-``MACE`` sibling this anchor *is* produced by the training
CLI, because ``ScaleShiftMACE`` is exactly what the CLI emits and pinning the
class a user actually gets is the point. The command is built here as an
explicit argv list and recorded verbatim in t... |
61741611a82d5424a6962a190156a0d436074256496405bfebeb48b1f1905262 | Python | 9,718 | 282 | ###########################################################################################
# Higher Order Real Clebsch Gordan (based on e3nn by Mario Geiger)
# Authors: Ilyes Batatia
# This program is distributed under the MIT License (see MIT.md)
#######################################################################... |
bfcd58936a848c6224f73d245e6100370a990cc789bebc618fbf61103881c66c | Python | 9,726 | 258 | #!/usr/bin/python3
###
# Script for the control of phase 3 of training. This builds on the base ArduinoComm.py
# scripts, and automates trials that show the cue and with appropiate sequence of goal events.
# option includes to change the if there's a light at the reward well when cue present.
###
import os, sys
impor... |
2b353229794055ec2748bb31230c6aa96c0f8aea6a216e181241c45089832b20 | Python | 9,729 | 308 | import argparse
import logging
import os
from typing import Dict, List, Tuple, Union
import torch
from e3nn import o3
from mace.modules.wrapper_ops import CuEquivarianceConfig
from mace.tools import deprecation
from mace.tools.cg import O3_e3nn
from mace.tools.cg_cueq_tools import symmetric_contraction_proj
from mace... |
b197bd35422dcce7a46bb965a13032ffc1909b65ea61af72cc4b982589992929 | Python | 9,733 | 184 | # %%
import os
import numpy as np
import time
import h5py
import sys
from scipy import sparse
from scipy.io import savemat, loadmat
import multiprocessing as mp
sys.path.insert(1, '../..') # the path containing "suns" folder
os.environ['KERAS_BACKEND'] = 'tensorflow'
# os.environ['CUDA_VISIBLE_DEVICES'] = '0' # Set w... |
c3007a43ebf942be6fdfedc995a2f2709c9b76851d464163fabb73bd853224d2 | Python | 9,744 | 250 | """
Pure-torch gated equivariant nonlinearity, drop-in replacement for e3nn nn.Gate.
Eliminates graph breaks caused by:
- if gates.shape[-1]: (data-dependent control flow)
- _Sortcut / Extract (fx.Graph codegen with dynamic slicing)
- ElementwiseTensorProduct (TorchScript)
Supports both mul_ir (e3nn default) an... |
6e26cdcb78be1a2917784d60fb72d74290831da7e67ce57b2066e54526328369 | Python | 9,748 | 266 | # 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
#
# Unless required by appli... |
fb37fddf9914dda9c00297cf71c1d6dae8458168b489b49316a057803af44553 | Python | 9,751 | 286 | import torch
import os
import numpy as np
import pandas as pd
import pytorch_lightning as pl
from rdkit import Chem
from torch.utils.data import Dataset as TorchDataset
from torch_geometric.data import Data as GeometricData
from torch_geometric.loader import DataLoader as GeometricDataLoader
from sklearn.preprocessing... |
0db6e033adfd22ace1a3b79877e4cabb0c710b401f9742bccba92a8dea637fa1 | Python | 9,753 | 263 | import numpy as np
import torch
from nequip.data import AtomicDataDict
from nequip.data import (
DataStatisticsManager,
EnergyOnlyDataStatisticsManager,
PerAtomModifier,
EdgeLengths,
NumNeighbors,
)
from nequip.data import (
Count,
Mean,
RootMeanSquare,
StandardDeviation,
Max,
... |
a4a55a06df57cf8301774a23bf86eb4ace902a8ce19aaabe0e5240ec7791c876 | Python | 9,758 | 207 | """
Functional Alignment
====================
When performing any type of group analysis, we assume that each voxel is
reflecting the same computations across all participants. This assumption is
unlikely to be true. Several standard preprocessing steps assist in improving
'anatomical alignment'. We spatially normaliz... |
7dab43293faa58375d23147d93c6c6624e2946c5759af0255b730db83f59ef02 | Python | 9,763 | 320 | """
Provide facilities for multiprocess logging, logging exception, logging handlers for session log files
and socketio logging.
Author: Tal Eisenberg, 2021
Starts a listening thread that receives log records from other processes, and outputs them through the
main process. Processes should call logger_configurer() fro... |
382ecd0ee15ca9677976302955459a533c71b7570c3815ce62c9de0f0e3316f3 | Python | 9,765 | 258 | #!/usr/bin/python3
###
# Script for the control of phase 2 of training. This builds on the base ArduinoComm.py
# scripts, and automates trials that show the cue and with appropiate sequence of goal events.
# option includes to change the if there's a light at the reward well when cue present.
###
import os, sys
impo... |
312c2609cfdc971289a178e41e6b8ffbf5c85480d5df00a0206eb26d88c9b746 | Python | 9,767 | 310 | from __future__ import print_function
from __future__ import division
import os
import sys
import json
import csv
import multiprocessing as mp
import math
import pandas as pd
from pandas.io.json import json_normalize
from Bio.Seq import Seq
# Minimal number of nucleotides to make alignment
MIN_NUC_V = 5
MIN_NUC_J ... |
352ad40df9dc913c446905bdcc6eea206235f153de5d8c1f574b2b335fb4a97b | Python | 9,768 | 267 | import math
import einops
import torch
import torch.nn as nn
from einops.layers.torch import Rearrange
from model_angelo.gnn.backbone_distance_embedding import BackboneDistanceEmbedding
from model_angelo.models.bottleneck import Bottleneck
from model_angelo.models.common_modules import FcResBlock, SpatialAvg, LayerNo... |
f3ab2108f087cfe7201a4b8ede266db05c0bf7e3c4f82aeab0ef2cd2266baae3 | Python | 9,774 | 241 | import matplotlib.pyplot as plt
import numpy as np
import pickle
from aux_fun import get_selected_features
import pandas as pd
import seaborn as sns
# --- Bar plot with SS and FPR/h for each patient considering all SOPs---
def fig_performance(patient, SOP_list , info_test, approach):
# Information
... |
04e79ab69ffcce9590f232204be790b63aaa2c6a552c5690a9d2e746c30f0bdb | Python | 9,777 | 244 | """Wrapper for NequIP framework models in torch-sim"""
import torch
import torch_sim as ts
from torch_sim.models.interface import ModelInterface
from nequip.data import AtomicDataDict
from nequip.data._nl import NEIGHBORLIST_BACKEND_ALCHEMIOPS
from .mixins import _IntegrationLoaderMixin
from collections.abc import... |
7b14d12d725629e128bd4469ae8e5df14ad9cf89e4a0223858f5131b885fe0d7 | Python | 9,781 | 313 | import numpy as np
# import matplotlib.pyplot as plt
import torch
import h5py
import torch.nn as nn
from torch.utils import data
import itertools
# number of available gpu
ngpu = 1
batch_size = 16
dataRoot = "../../data"
labelFiles = "labels-1.h5"
matFiles = "matrices-1.h5"
labelsh5 = h5py.File(dataRoot+"/"+label... |
85fc7debcd80979d9adfddd0782b79b6216566925cba6d8a0f766bc6a6b264b1 | Python | 9,781 | 308 | import os
import string
from collections import namedtuple
from itertools import islice
from typing import List, Tuple
import warnings
import numpy as np
from Bio import SeqIO
FASTASequence = namedtuple("FASTASequence", field_names=["seq", "rep", "chains"])
class FASTAEmptyError(RuntimeError):
def __init__(sel... |
749d82099110923108c0c355e733599869175983d547d1bd408c49471d7d0fb2 | Python | 9,782 | 255 | from __future__ import annotations
import argparse
from pathlib import Path
from typing import Any, Sequence, cast
import attrs
from typing_extensions import override
from snakebids import bidsapp
from snakebids.plugins.base import PluginBase
from snakebids.types import OptionalFilter
from snakebids.utils.utils impo... |
983cb0021c3b99bbc4dadb4205c0758c4c37db3d441c3f4c7b888998476f5fee | Python | 9,782 | 234 |
import os
import pickle
import random
import numpy as np
import pandas as pd
from sklearn.preprocessing import StandardScaler
import torch
from torch.utils.data import Dataset
from hyper_dti.settings import constants
from hyper_dti.utils.bio_encoding import precompute_target_embeddings, precompute_drug_embeddings
... |
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