sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b8865080ddd404311949c5406bf513d2ae5cad85a9accaa8c7f59fb54c3af09f | Python | 7,781 | 205 | # Copyright (c) 2017-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 os
import sy... |
4af0ce46c9b7af8e93864902f12d48c316394ff1e31ade40ca261387a15eab91 | Python | 7,782 | 196 | # 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.
from typing import Dict, List, Optional, Tuple
import torch
import torch.nn as nn
from torch import Tensor
from fairseq import utils
from fa... |
40a8699e2f9e4d46728f040c2aded4f6b5bba729cd907d5d75c4d1ce825bb8d4 | Python | 7,788 | 266 | import torch
import utils
import numpy as np
import torch.nn.functional as F
from torch.utils.data import DataLoader
from torch.nn.modules.loss import _WeightedLoss
from sklearn.metrics import roc_auc_score
def collate(batch):
protein_list = []
label_list = []
info_list = []
id_list = []
device ... |
7388b1a2bc3477c8b9121451c1677aa3d0affa882bd02280175904bf0135b6aa | Python | 7,790 | 229 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import sys
from openfl.experimental.workflow.interface import FLSpec, Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from openfl.experimental.workflow.placement import aggregator, collaborator
cl... |
73332cb43f16f9814ca2d7fe725d67fe762dca863f857cd6e772febec43c6570 | Python | 7,796 | 209 | """
Created on Tue Jun 15 16:14:39 2021
@author: Mathieu Scheltienne
"""
from abc import ABC, abstractmethod
import cv2
import numpy as np
from matplotlib import colors
from screeninfo import get_monitors
from ... import logger
class _Visual(ABC):
"""
Base visual class.
Parameters
----------
... |
83485d69a9c4e0a9bd95e47b6644e7a8ca0e4c09d586315c70ecb039124fbc10 | Python | 7,797 | 213 | from configuration import *
from spikeinterface.sortingcomponents.benchmark.benchmark_motion_interpolation import BenchmarkMotionInterpolationMearec
from spikeinterface import compute_sparsity
import MEArec as mr
import numpy as np
from plotting_tools import removeaxis, label_panel
from figure_estimation import dri... |
945bbaa70aead8bfad0fc6876e3daa46d302afa7a13dc864b7652ed662bd6df4 | Python | 7,797 | 238 | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import math
import torch.nn.functional as F
from torch.utils import data
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset
from ssc_datase... |
39bf283ff6cc2bd34acf75925eb902489133dd4698140531e2792a493684ca2e | Python | 7,799 | 238 | """Unit tests for mace/tools/arg_parser.py.
We test the *contract* of the parsers, not every one of the ~200 flags:
* ``build_default_arg_parser`` builds and parses a minimal valid command line
(only ``--name`` is required).
* Critical defaults the rest of the codebase relies on (dtype, device, model,
loss, cutof... |
006a3eb5db67fc3b61bc32281e172e4306efb4fe57a140088137b99575c0a08e | Python | 7,801 | 231 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 23 11:25:14 2021
@author: nicol
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
import time, os, glob
from tqdm import tqdm
import numpy as np
from skimage.io import imread
import seaborn as sns
import pand... |
7c8190070640c53be26cdc95e682bad5e4258fa5b41f7b4da1f423b5adffc131 | Python | 7,801 | 189 | """
This is the data preprocessing that should return
the .pt with the data to run the model
TO BE EXECUTED FROM MAIN FOLDER (relative paths)
"""
import os
import pandas as pd
from scipy.sparse import csr_matrix
import json
import argparse
from rdkit import Chem
from rdkit.Chem import Descriptors
import torch
fro... |
508410736011a8d611e771b21248649e91b1becb1cdcff0dd931b69f5bc7fc2d | Python | 7,809 | 234 | from functools import partial
from PyQt5 import QtWidgets, QtGui, QtCore
from sanpy.sanpyLogger import get_logger
logger = get_logger(__name__)
EDITABLE_SPIKE_RESULTS = ("spike_condition", "userType", "spike_include")
import sanpy
from sanpy.interface.plugins import sanpyPlugin
class ComboBox(QtWidgets.QComboBox... |
66a6b3b1610e66198392c1d351a421691d5dfe78dd62168379d05d3d58834e2a | Python | 7,813 | 204 | """
Non-linear Oscillator Entrainment
=================================
In this tutorial, we will examine entrainment of a
`Van der Pol oscillator (VPO) <https://en.wikipedia.org/wiki/Van_der_Pol_oscillator>`_ that receives oscillatory input
from a simple `Kuramoto oscillator (KO) <https://en.wikipedia.org/wiki/Kuramo... |
e7274118159c4e4df45e3baf9c5b067cba00f9407e93b1f5e3d9f46fb2d71c82 | Python | 7,823 | 222 | """Tests for runtime-owned detection and analysis-result definitions."""
import uuid
import pytest
from pydantic import ValidationError
from sanpy.bAnalysisResults import (
AnalysisResults,
get_analysis_result_definitions,
get_plot_result_definitions,
new_result_values,
)
from sanpy.bDetection import... |
e3dbca8284afc90002b71da8854d5860c58707da6b4ec80c32275349de2375f8 | Python | 7,826 | 237 | """Create and reopen local-only DANDI Dandisets of SanPy NWB files."""
from __future__ import annotations
from collections.abc import Mapping, Sequence
from dataclasses import dataclass
import os
from pathlib import Path
import re
import tempfile
from typing import Any
from pydantic import BaseModel, ConfigDict, fie... |
1b50a0ca02a30fab1dace169d5ab494b2d708fc3d5a9944413d86f898418760a | Python | 7,827 | 204 | """
Non-linear Oscillator Entrainment
=================================
In this tutorial, we will examine entrainment of a
`Van der Pol oscillator (VPO) <https://en.wikipedia.org/wiki/Van_der_Pol_oscillator>`_ that receives oscillatory input
from a simple `Kuramoto oscillator (KO) <https://en.wikipedia.org/wiki/Kuramo... |
552ee22adc869a6c61e89d5c7b2813c865bca80a5901418e40526345f2e1051e | Python | 7,827 | 209 | # 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... |
b85574cf67d4e1bd9aa382dc56f8705445e5e921de1c2c83fab5f8fc7b97ba0f | Python | 7,830 | 235 | ###########################################################################################
# Checkpointing
# Authors: Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
###########################################################################################
import dataclasses
import loggi... |
ad832258b2e1598fe1546200e23f9a0be45d154af8e3c2f10cb3e802a74848d9 | Python | 7,835 | 229 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
import scipy.signal as sig
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from matplotlib import cm
# main program
if __name__ == "__main__":
# Define paths to compare
datapath = "/home/nikos/Documents/projects/Python/memstim-hh/... |
c4d82452a1004c439ee928f4281ccdc6ea7714a5e9b33d0ea80d468454e4d4b9 | Python | 7,837 | 180 | """The published MACE-Polar model reproduces its committed reference.
ELEC-2 rebuilds ``PolarMACE`` on the new architecture and converts this
checkpoint onto it; this file is the number it has to land on. What is pinned
is the whole surface the calculator exposes -- the energy/force/stress side
*and* the electrostatic... |
25dd248d40a183e83c3db1c94e199a41fb27db82a13ce27d96a2cecc1507c813 | Python | 7,838 | 196 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import glob
import numpy as np
from data_functions import load_data, TwoPopAlignmentFormatter, load_data_slim, read_slim_out
from mpi4py import MPI
import h5py
import matplotlib.pyplot as plt
# use this format to tell the parsers
# where to insert ce... |
53d1b347bbc6f2fd26769956549e504b040ed94ac5adb6ad63ee1589b45f94ff | Python | 7,840 | 178 | import os
import tensorflow as tf
import multiprocessing as mp
# from https://github.com/oxpig/kasearch/blob/main/kasearch/canonical_alignment.py
CANONICAL_NUMBERING = ["1 ", "2 ",
"3 ", "3A",
"4 ", "5 ", "6 ", "7 ", "8 ", "9 ", "10 ", "11 ", "12 ", "13 ", "14 ", "15 ", ... |
67cbf2b87737d7d1326df1f0ae56471dd1344e0884c2bbc36053925b59374831 | Python | 7,840 | 177 | import pandas as pd
import torch
from torch.utils.data import DataLoader, TensorDataset
from sklearn.metrics import confusion_matrix, classification_report, precision_recall_fscore_support
from scipy.interpolate import interp1d
import math
from modelClasses import *
from utilityFunctions import *
os.environ['CUDA_LAUNC... |
1c07f89e55f0958a0bccbf9ae041d0ff60632df28825e0bcfd31f43cc17db143 | Python | 7,844 | 194 | import chromadb
import chromadb.test.property.invariants as invariants
import chromadb.test.property.strategies as strategies
import copy
import hypothesis.strategies as hyst
import logging
import pytest
from chromadb.api.models.Collection import Collection
from chromadb.test.conftest import (
reset,
skip_if_n... |
995e89fe2287f942b2b9ba683c50d1136158615db0848ba5e294d3df4508f93b | Python | 7,844 | 201 | """Spatial RSA computes ordinary stacks with explicit external mapping."""
from __future__ import annotations
import nibabel as nib
import numpy as np
import pytest
from nltools.data import Adjacency, BrainData
def _atlas_for(bd, n_rois=2):
"""Return a labeled atlas Nifti aligned with bd.mask, partitioning the... |
523e9ff6f10665efa1cf908bdee7be57b37fcea535694656f085b288896a8e19 | Python | 7,845 | 162 | import dill as pickle
import pandas as pd
from sklearn import model_selection
from sklearn.utils import resample
import numpy as np
import logging, coloredlogs
from collagen.data import Splitter
coloredlogs.install()
class HiarFoldSplit(Splitter):
def __init__(self, ds: pd.DataFrame, train_size_per_class: int, ... |
5ed78a6191e0f739beb7e8d3b035e494748417ac267dca3f98ce18e3c3d65f13 | Python | 7,848 | 191 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_scatter import scatter
from torch_geometric.nn import global_add_pool, global_mean_pool, global_max_pool, GINConv
class Readout(nn.Module):
def __init__(self, node_feat_dim, node_hiddens, graph_hiddens, use_gate=True, pool_type='add'):
... |
ce8c09b8d318ae367c424faa4d6a9fb798f2ae48af4fef2a3370ab4342fcf050 | Python | 7,848 | 191 | # /usr/bin/env python3
# coding: utf-8
#
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law and abi... |
0fbfd97081a01780407c2042b1377541bef78c283268d80b1ccae549f7c29ed5 | Python | 7,852 | 249 | """
Implementation of dFC methods.
Created on Jun 29 2023
@author: Mohammad Torabi
"""
import time
import numpy as np
from joblib import Parallel, delayed
from scipy import signal
from sklearn.covariance import GraphicalLasso, GraphicalLassoCV
from ..dfc import DFC
from ..time_series import TIME_SERIES
from .base_d... |
be5b6e9adc03ae1341f20b762348acbe92697a01c18794deb0c0e6f0a7da92c4 | Python | 7,853 | 222 | """Visualise the uncertainty of the empirical Fréchet mean on the sphere.
The variance of the Fréchet mean FM_n of a sample of n IID random variables
of variance Var is decreasing more slowly in a sphere than in a Euclidean
space. This example computes the modulation factor
alpha = Var( FM_n) / ( n * Var)
for is... |
019457c97a3b9176a34a696de2baf4399087bd7cb6e1f012877350621f61bb56 | Python | 7,854 | 223 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .df_utils import one_hot_argmax
class ST_Net_Sigmoid(nn.Module):
def __init__(self, input_dim, output_dim, hid_dim=64, num_layers=2, bias=True, scale_weight_norm=False, sigmoid_shift=2., apply_batch_norm=False):
super(ST_Net_Sigmoid, s... |
67fe197015f62507918f744834df950c8a11143c8e4ddb1a64fd5af7e542eaf2 | Python | 7,854 | 188 | """Dataclasses to hold transformed and aggregated result from components."""
from __future__ import annotations
__all__ = ["ComponentResults", "SmilesAssociatedComponentResults"]
from dataclasses import dataclass, field
from typing import List, Dict, Optional, Set
import numpy as np
@dataclass
class SmilesResult:
... |
456c6a42a72fb4ecd10da1783b00bb6036fe27f8ca59957189ab6e53b4d6fc70 | Python | 7,856 | 217 | # bi-directional srnn within pkg
import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import math
import torch.nn.functional as F
from torch.utils import data
from SNN_layers.spike_dense import *#spike_dense,readout_integrator
fr... |
1174b6459012875f42d9148338334db7efd7203958a6c0586ed24d8c0a9a373a | Python | 7,860 | 205 | # ==============================================================================
# Copyright 2025 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
#
# Convert 2D data (generated with Matlab) to 3D data format (separate H5 files per source)
imp... |
7de0c239b0e0bb5f68b9ffd30acab38d1d732f0ff8c502e12a9673415d400feb | Python | 7,864 | 228 | """`mace_plot_train` against a real results log.
The plotting CLI had no test at all, and the results log format it parses had
none either, so nothing connected the two: `mace_run_train` is free to rename a
column and the only symptom is a plot nobody generates in CI.
That absence was hiding a CLI that could not run.... |
8ef154709b7770eb065798c061f08b5eaf8855aabc6043efdfbf007a34cd9d02 | Python | 7,867 | 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... |
9cecfcbee219be7d435390513f5f6c699b2b869744e10fa298899fe66c90cd33 | Python | 7,872 | 173 | from __future__ import print_function
import os
import sys
from argparse import ArgumentParser, RawDescriptionHelpFormatter
from argparse import ArgumentTypeError
from .core import process_file
def run(filename, output=None, model_capacity='full', viterbi=False,
save_activation=False, save_plot=False, plot_... |
ccfe97a7229302a783acf07f853eaf28b690bd5ea64cad07d851b2f666995dd5 | Python | 7,872 | 211 | """Multi-stage learning with RL"""
from __future__ import annotations
import logging
import torch
from reinvent.utils import setup_logger, CsvFormatter, config_parse, get_tokens_from_vocabulary
from reinvent.runmodes import Handler, RL, create_adapter
from reinvent.runmodes.setup_sampler import setup_sampler
from re... |
67368310391d5011b3e0da9963ad40a32b5009c5b8dfd5869656ddb560a6bba5 | Python | 7,877 | 136 | import os
import torch
from pytorch_lightning import Trainer
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
from pytorch_lightning.loggers import TensorBoardLogger
from metrics import Metrics
from models.lightning_rnn import LITGRU
from modules.data_module import FireflyDataModule, RealFireflyDa... |
571f07b291d47337d171203dd00a6fd58010b5aa3b7825ca19ba486eddad9bfa | Python | 7,879 | 190 | """
gathering the accuracy as a function of time (changing due to memristive drift)
"""
from SHIP import TensorHauler,network,liN,inputN
from braille_task_utils import (load_braille_dataset,
delta_encoding,
select_datasets)
from torch import (tens... |
cc2b6d1f12bac7460ac63b7d0ee13bad13864d00e7bbf651d1510eda49d1459b | Python | 7,879 | 234 | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import math
import torch.nn.functional as F
from torch.utils import data
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset
from ssc_datase... |
44792e9f2759aa82a4fd3ff268e0da63d7219c39bc0b7968f265d981302fcbc4 | Python | 7,882 | 231 | """
Benchmark: legacy scalar-edge API vs. new PopulationTemplate + Connectivity API.
Network: N Wilson-Cowan excitatory nodes, all-to-all coupled with a random
weight matrix W (diagonal = 15.0, off-diagonal ~ N(0, 1/sqrt(N))).
Run with:
conda run -n sbi python examples/benchmark_population_connectivity.py
"""
im... |
fb77e3d5756f704d5e208efdce36978f724a6ce6eb92a7eee924cd38bda5cfee | Python | 7,889 | 256 | import torch
import torch.nn as nn
import torchvision.transforms as transforms
import torchvision.datasets as dsets
import torch.nn.functional as F
import numpy as np
from torch.autograd import Variable
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import matplotlib.pyplot as plt
import math
from sklearn.util... |
43fbd2f53e024c2bfafef99fa59ad5883d7a2f0538a890b416cc893165c50bb9 | Python | 7,899 | 246 | """The manifold of positive reals.
This manifold is a particular case in dimension 1
of the SPD matrices endowed with the SPD affine-invariant metric
with a power affine coefficient equal to one.
This manifold is used as part of a product manifold involving
complex Poincare disks to classify complex stationary centere... |
8a1166a0b98e7757712d16068c002e6434e561715d9a0869681edae4bc1b76bb | Python | 7,901 | 262 | """
Data logging processes
Author: Tal Eisenberg, 2021
"""
import csv
from datetime import datetime
from pathlib import Path
import multiprocessing as mp
import rl_logging
import database as db
from video_stream import ImageObserver
import managed_state
from configure import get_config
class DataLogger(mp.Process):... |
928f68bd3850aaf7b5a38e0eedc84168e6ae553457d821c35e83e005865e9ebe | Python | 7,902 | 251 | from __future__ import annotations
import re
import sys
from typing import (
TYPE_CHECKING,
Any,
AnyStr,
Container,
Dict,
Generic,
Hashable,
Iterable,
Iterator,
Sequence,
SupportsIndex,
TypeVar,
overload,
)
from typing_extensions import Self, override
_T = TypeVar(... |
a893564bf0acdd027c390db9c6502f6a3c206928a9ef7cc07a8018a672de6e61 | Python | 7,903 | 201 | # ##############################################################
# This file is received from
# https://github.com/DmitryUlyanov/deep-image-prior/blob/master/models/unet.py
# It is the implementation of the following study:
# https://arxiv.org/abs/1505.04597
# The code is licenced under Apache 2.0 licence
# https://git... |
a178b5c270c4608b7a3c90681b63a2af2b770c8a53a2dab85de7c25e54214808 | Python | 7,905 | 235 | import os
import torch
import matplotlib.pyplot as plt
# torch.multiprocessing.set_start_method('spawn')
os.environ['CUDA_VISIBLE_DEVICES'] = "2"
print('todo 0502: benchmark for pretrained_models')
# to maintain the same parameter configuration
saving_name = 'tiny_snn_room_epoch100_origin_exp4_seq5_time5ms_3layer_test... |
dc92fc9fca1aa8ef9a2bb86af4a66dd981195c4167cb1d20a86059eb83c20709 | Python | 7,906 | 264 | import os
import pickle
import random
from collections import OrderedDict
from glob import glob
import numpy as np
import torch
LEADSETS = {
12: ["I", "II", "III", "aVR", "aVL", "aVF", "V1", "V2", "V3", "V4", "V5", "V6"],
8: ["I", "II", "V1", "V2", "V3", "V4", "V5", "V6"],
6: ["I", "II", "III", "aVR", "aV... |
e7f705b52e3f88bdcdb9a00a9e6233c915a4dd9467068deea3a62c9fe8f678d4 | Python | 7,912 | 239 | """Vocabulary helper class"""
import re
import numpy as np
class Vocabulary:
"""Stores the tokens and their conversion to one-hot vectors."""
def __init__(
self, tokens=None, starting_id=0, pad_token=0, bos_token=1, eos_token=2, unk_token=None
):
self._tokens = {}
self._current_... |
ec0e10c71a51ed11099772b32fdbdce0893d1e36641c40532cbaad736e03653c | Python | 7,912 | 198 | """ Sliding-window module
Sliding-window analysis. The code is a python adaptation
from the code used by Vasa et al. (2018).
It outputs a spreadsheet for each window, where the IDs of
that window and the sorting variable are output. It also
outputs some descriptive stats for the sorting variable in
each window.
"""
... |
e0932b72c55c2393f1df708a6aaabbfaf252fc247ff2cec394e625cd47ca2951 | Python | 7,913 | 246 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""STCPipelinemodule."""
import copy
import gzip as gz
import numpy as np
from openfl.pipelines.pipeline import TransformationPipeline, Transformer
class SparsityTransformer(Transformer):
"""A transformer class to sparsify input dat... |
b99f70579120a583bb8acbc359c4f2508f78e20254b48d6a220628a32a357ee4 | Python | 7,919 | 205 | #### pyClusterROI_test.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 is a demonstration of how to use the
# toolbox and a regression test to make sure that the toolbox code... |
2a4399c43a9641f4c9fb8e4a6fec54bac5ad1a01a1dae782f339f10b71efc68c | Python | 7,923 | 157 | # %%
import os
import numpy as np
import time
import h5py
import sys
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 which GPU to use. '-1' use... |
c33bfe5383eb45e91478a7cb1a0de3a99e119373a0a61c5324c135f22aaa7957 | Python | 7,927 | 263 | """
Data logging processes
Author: Tal Eisenberg, 2021
"""
import csv
from datetime import datetime
from pathlib import Path
import multiprocessing as mp
import rl_logging
import database as db
from video_stream import ImageObserver
import managed_state
from configure import get_config
class DataLogger(mp.Process)... |
0916a0dc139e2e5bd392ef5d998806ad05b38575675a1ef9d896bfab7a8d3fa6 | Python | 7,936 | 247 | """Module exposing the GeneralLinear group class."""
import geomstats.algebra_utils as utils
import geomstats.backend as gs
from geomstats.geometry.base import VectorSpaceOpenSet
from geomstats.geometry.lie_algebra import MatrixLieAlgebra
from geomstats.geometry.lie_group import MatrixLieGroup
from geomstats.geometry.... |
9827e679de4da0c62311708eabce886cd0c649530da39cf95e07d5c25715f326 | Python | 7,946 | 194 | """ ICC subject and task
"""
from argparse import ArgumentParser
import warnings
import re
import os
import numpy as np
import pandas as pd
import pingouin as pg
def main():
""" Launching ICC analysis
"""
print('---------------------------------------------')
print('-------Edge-wise Intraclass Correla... |
6f2c2ed5981601f6b0a29ae1611108589af5ac75f0a650a47880542c91acea45 | Python | 7,950 | 242 | """
Count secondary structures in a PDB file as determined by p-sea
https://www.biotite-python.org/apidoc/biotite.structure.annotate_sse.html
"""
# Examples:
# python ~/projects/protdiff/bin/annot_secondary_structures.py sampled_pdb/*.pdb plots/ss_cooccurrence_sampled.pdf
# python ~/projects/protdiff/bin/annot_second... |
3170de7de568f9f72bae5feb0af21f3c37a31a7dcf7038f75a42e7a424ec2284 | Python | 7,952 | 215 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as N
import os
from sklearn.linear_model import LinearRegression
from sklearn.metrics import explained_variance_score
from sklearn.model_selection import KFold
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from s... |
d8611e3bd34613f694ed45448fdacefab0bd9af79a6485ebf45115ccd96e730c | Python | 7,953 | 167 | """Derived identifiers for the levels above and below a curated record.
A record is a receptor against a presented peptide, and both halves recur across records, so each
half needs a name of its own. Four levels do, and all four key on content that has no separate
existence: there is no such thing as a clonotype apart... |
93ebaa4940585fb676ee1e56ab2cbae65cd5c8b85911936b16efa2861752bed5 | Python | 7,956 | 229 |
from pathlib import Path
import imageio.v2 as imageio
import matplotlib.pyplot as plt
import numpy as np
import ppafm.ml.AuxMap as aux
import ppafm.ocl.field as FFcl
import ppafm.ocl.oclUtils as oclu
import ppafm.ocl.relax as oclr
import torch
from matplotlib import cm
from ppafm.ml.Generator import InverseAFMtrainer... |
66ce0a5d4e84e2b06b5da423d6adea3733f7926c018f3575eb5ceeaa623096ba | Python | 7,957 | 201 |
# -*- 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... |
4cee0caa44cf510e6291e4e8d9f4e056d69bda37d2b8b88c3560b1e59c1e76ad | Python | 7,960 | 250 | # 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... |
8675dec900130e81a8f158620059393bfa0cb7d2b4a6e7f05295b7ae032409ba | Python | 7,966 | 268 | """Code to construct the VLAAI network.
Code was extrcted from https://github.com/exporl/vlaai
"""
import tensorflow as tf
def extractor(
filters=(256, 256, 256, 128, 128),
kernels=(64,) * 5,
dilation_rate = 1,
input_channels=64,
normalization_fn=lambda x: tf.keras.layers.LayerNormalization()(x),
... |
4193780384d88a3d75134b4bfbe781a9e4facdcbcbbd3ac1d8037fcbbbcd43d9 | Python | 7,967 | 257 | import community
import markov_clustering as mc
import networkx as nx
from scipy.sparse import csr_matrix
import torch
from torch_scatter import scatter_max, scatter_mean
from torch_geometric.nn.pool.pool import pool_edge, pool_batch, pool_pos
from torch_geometric.nn.pool.consecutive import consecutive_cluster
from to... |
d3b537785cd9fcd1d85dd97008ce6a03a7826fa18e46648090b7db073100b2e5 | Python | 7,968 | 179 | import math
import json
from openpyxl.worksheet.table import Table, TableStyleInfo
from openpyxl.styles import Alignment
from nilearn import plotting,image,surface,datasets
from utilityFunctions import *
import collections
bn_atlas_file = 'PROJECT_DIR/scripts/features/bnatlas_tree.json'
parent_substitutions={
'Am... |
7cbf0d1c101372e689be74f56d64c4645076c61b345812422fd3465cda5e9255 | Python | 7,969 | 220 | # 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.
from dataclasses import dataclass, field
import torch
from fairseq import metrics, utils
from fairseq.criterions import register_criterion
fro... |
3d7b0ca22d6971d5a6c5eb2648f13c818eb4621817c50e680ea78a34db9e6607 | Python | 7,972 | 209 | from torchvision.datasets import ImageFolder
from typing import Optional, Tuple, Dict, List, Union
import torch
import argparse
from utils import logger
from .. import register_dataset
from ..dataset_base import BaseImageDataset
from ...transforms import image_pil as T
from ...collate_fns import register_co... |
75105a25694f1aeb386f3a17a17934ad76b1948abe8eb71a638ff7aab38d5fff | Python | 7,974 | 195 | """ Pyramidal CAN """
""" ------------------------------------------------------------------------ """
py_CAN_inp_eqs = '''
dv/dt = (- I_CAN - I_M - I_leak - I_K - I_Na - I_Ca - I_SynE - I_SynExt - I_SynI - I_SynHipp + r_drive*I_exc + rin*I_tonic + r*I_stim) / ((1.*ufarad*cm**-2) * (size)) + noise : volt
I_CAN ... |
b3ed13a2237f14fc0c6aa6069f5b23e28edfd6607fc289abea88a1c96bd573b4 | Python | 7,977 | 216 | """The `--wandb` flags, exercised without a Weights and Biases account.
Nothing exercised any of the six. They are the flags whose failure mode is a run
that trains fine and logs nowhere, or logs under the wrong project, and neither
shows up as an error.
Two levels. `setup_wandb` is where five of the flags become arg... |
12c97d0e8b0bf024ce24e4de8d99c4446b26db4e4bc8ecb5c2bc936cd633a22c | Python | 7,978 | 195 | import copy
import numpy as np
import struct
def fill_pul_with_data(pul, fh, group_idx, series_idx):
"""
Fill the ["data"] field of all pulse tree records for the specified group and series with raw data from file.
The record header contains the starting bit of the raw data, and parameters for its reconst... |
58dfcb22053664d80f654dfc9d483e7e0ebe68b06e5cfd39d1d642334fa47fe5 | Python | 7,981 | 144 | """Produce record confidence v3 from completed tables and a frozen Bayesian model."""
from __future__ import annotations
import gzip
import hashlib
import json
from importlib.resources import files
from pathlib import Path
import polars as pl
from ..emit.vdjdb3 import read_table
from .bayes import score_records
from... |
f8b387963f37d55ef551c5e95808356c16289ce9917b8dd541a4cdd27b220a11 | Python | 7,989 | 183 | # -*- coding: utf-8 -*-
# /usr/bin/env python3
#
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law... |
1c01afe6cff778aa6381b83273ed615d7b8ff7e2368b6875853a5906f2c2af4e | Python | 7,990 | 182 | import torch
from torch import nn
import torch.utils.data as Data
import torch.nn.functional as F
from torch.autograd import Variable
import numpy as np
import copy
import math
import collections
# torch.manual_seed(1)
# np.random.seed(1)
class LayerNorm(nn.Module):
def __init__(self, hidden_size, variance_epsilo... |
95cd1d2fb2db27b0c501d4913429ecc1bb21e50c090bab02044aa35c090a64ee | Python | 7,999 | 140 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this sof... |
25c1968fb1684a2579a217914d6f3459cd36bacfcebd4c0db46764c3ae4e2739 | Python | 8,000 | 201 | import statistics
import os.path
import numpy as np
from common.common import load_pickle
from safe_msmt.configuration import DATA_FOLDER, OUTPUT_FOLDER
from common.evaluation.measures import get_binary_classification_measures, get_multitask_classification_measures
iucn_status = \
{
0: ("little spiderhunter", "least ... |
c18e3048062ef39a978f18064ff9d7961fcda2ead5a70641b33fb310fabbe287 | Python | 8,002 | 231 | # 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 applic... |
cc6beb3444c38d9051655fe4a041f030d84bd7b74dc5c2b4b56db56d5c532fb1 | Python | 8,002 | 206 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as N
import os
from sklearn.linear_model import LinearRegression
from sklearn.metrics import explained_variance_score
from sklearn.model_selection import KFold
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from s... |
9bdae09d1b68b283f980fbad0fa3510844de179ab98e90216e027efc7dae6135 | Python | 8,003 | 183 | # 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 ... |
04e1440dcef5a46cfdd84b0feaa381b87e25c4e933f7afa1e2a2249c0c70e014 | Python | 8,004 | 159 | # %%
import os
import numpy as np
import time
import h5py
import sys
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 which GPU to use. '-1' use... |
fc7ce809beeb8478847f91d8df2fe557601d5c8f720f1097a5ca0277c25707ed | Python | 8,008 | 252 |
from PyQt5.QtWidgets import QVBoxLayout, QPushButton, QLineEdit, QDialogButtonBox, QDialog, QMessageBox
from PyQt5.QtWidgets import QHBoxLayout, QGroupBox, QWidget, QComboBox, QStackedWidget, QLabel
class PreprocessingView(QDialog):
def __init__(self, app, control):
"""The view corresponding to co... |
f355b6ce39509880e6acd7c65ba2b5f938225d2347cfcdcd940bf1448793fbcd | Python | 8,011 | 223 | import tensorflow as tf
class TransformerBlock(tf.keras.layers.Layer):
def __init__(self, embed_dim, num_heads, d_hid, rate=0.5, use_bias=False, **kwargs):
super(TransformerBlock, self).__init__(**kwargs)
self.att = tf.keras.layers.MultiHeadAttention(num_heads=num_heads, key_dim=embed_dim, use_bias... |
85393095e3e6ea22d7564e45a520a96d42f6124749e88d2310d602de01738126 | Python | 8,017 | 181 | # Partial copy of the tensorflow python file image_ops_impl.py because loading this function per tf.image.psnr didn't
# work at the time.
import numpy as np
from tensorflow.python.framework import constant_op
from tensorflow.python.framework import dtypes
from tensorflow.python.framework import ops
from tensorflow.py... |
9b2d18886fd61090438ae2a2ff5478ddfcdc6bff56bfea1edf43dfba9ad66155 | Python | 8,017 | 203 | from ..abstract_dataset import AbstractDataset
import os
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.tri as tri
from mpl_toolkits.axes_grid1 import make_axes_locatable
from scipy.interpolate import CubicSpline
class AirfoilTransonicDataset(AbstractDataset):
parametric =... |
eb48a6f6dc3c5a693d249b43f44e86436162ce040294043e007ad5889f31c0ed | Python | 8,018 | 206 | """`--fixedpoint_update_config` and `--field_readout_config`.
Two CLI flags that choose which block PolarMACE builds and how, written as
dict literals in a string. They travel a path nothing tested: the string is
parsed by `_parse_literal_or_none`, handed to the constructor, and there a `type`
key is looked up in a re... |
91a090ecea466e09d320d4f55d8eeb25d9254c9c2affc5e8cb4dcf6e49c35ec7 | Python | 8,019 | 331 | import abc
import logging
from scipy.optimize import OptimizeResult
from torch.optim import LBFGS, SGD, Adam, RMSprop
import geomstats.backend as gs
from geomstats.numerics._common import params_to_kwargs
from ._optimization import Minimizer
class TorchMinimizer(Minimizer, abc.ABC):
"""Base class for torch.opt... |
a924c56d21ba7f06de07f236efe90ab061edcdf0ba141846313eafd34315387c | Python | 8,021 | 199 | # Copyright 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""This module contains the VerifiableDatasetInfo class."""
import json
from hashlib import sha384
from typing import List
from openfl.federated.data.sources.azure_blob_data_source import AzureBlobDataSource
from openfl.federated.data.sources.d... |
07c061af19802fafc6ebaa542d24a3eb99db4c1db477d6e0a09560e9ed2b814f | Python | 8,022 | 251 | import torch
from pymonntorch.NetworkCore.Behavior import Behavior
from pymonntorch.utils import check_is_torch_tensor
class InstantHomeostasis(Behavior):
def __init__(
self,
*args,
min_th=None,
max_th=None,
threshold=None,
gap_percent=None,
distance_sensit... |
141684cc226f267ebeda519f56a022e9fe3d95c51431806e1b76cfd9d5aa8681 | Python | 8,026 | 179 | import math
import json
from openpyxl.worksheet.table import Table, TableStyleInfo
from openpyxl.styles import Alignment
from nilearn import plotting,image,surface,datasets
from utilityFunctions import *
import collections
bn_atlas_file = 'PROJECT_DIR/scripts/features/bnatlas_tree.json'
parent_substitutions={
'Am... |
5aa48f815920c445cd18917f97fb7c9280a728baaf8660e41ea142102f533c43 | Python | 8,035 | 200 | import torch
def shift_by_int(img, x_shift, y_shift, is_res=False):
if is_res:
img = img.permute(0, 3, 1, 2)
x_shifted = torch.zeros_like(img)
if x_shift > 0:
x_shifted[..., x_shift:, :] = img[..., :-x_shift, :]
elif x_shift < 0:
x_shifted[..., :x_shift, :] = img[..., -x_shif... |
8bec06051984b16cd83608a977300ad84875e0c402c5aee8a1f1c40e57f5d900 | Python | 8,035 | 286 | from interval import interval
import numpy as np
# get usable segments from available interval lists
def seg_available(available, clip_length, neg = False):
seg = []
for a1, a2 in available:
length = a2 - a1
if length <= clip_length:
if neg == False:
seg.append([a1, ... |
51acf5f8be2277d0c77fff65718fc7eef2d9e345f86505c68a4673fb0666e1ce | Python | 8,037 | 209 | #### make_local_connectivity_scorr.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 constructs a spatially constrained
# Coefficient between the whole brain FC maps generaged ... |
50c5b5752abeb83a943f1adbd2a9395fb00b534496bb700f83fd17ce0245dbe8 | Python | 8,045 | 237 |
import scanpy as sc
import pandas as pd
import numpy as np
from scipy.spatial import *
from sklearn.preprocessing import *
import numpy as np
def res_search(adata,target_k = 7, res_start = 0.1, res_step = 0.05, res_epochs = 10,random_state=666):
print(f"searching resolution to k={target_k}")
res = res_start
... |
cd064cd4b31fe53bf3358d6c599b0ffd88fc3b2e208c9db91e3a4b6883493548 | Python | 8,045 | 222 | import torch
from pymonntorch.NetworkCore.Base import TaggableObject
from pymonntorch.utils import is_number
class Behavior(TaggableObject):
"""Base class for behaviors. All behaviors all `TaggableObject`s.
Attributes:
tag (str): Tag of the behavior.
device (str): Device of the behavior. Thi... |
6e067c34d51c45aad987a577b7dac85ec77a7ac68ed49e474016a7164866ca41 | Python | 8,047 | 260 | import community
import markov_clustering as mc
import networkx as nx
from scipy.sparse import csr_matrix
import torch
from torch_scatter import scatter_max, scatter_mean
from torch_geometric.nn.pool.pool import pool_edge, pool_batch, pool_pos
from torch_geometric.nn.pool.consecutive import consecutive_cluster
from to... |
020467e17c14729ab8f66677d388287fd258cafe9b8076831368ff4527dd4012 | Python | 8,050 | 271 | #!/usr/bin/env python3
import argparse
import matplotlib.pyplot as plt
import numpy as np
import odil
from odil import printlog
def u_init_smooth(x, y):
r = x**2 + y**2
res = np.exp(1 - 1 / (1 - r))
res = np.where(r < 1, res, 0)
return res
def u_init_blob(x, y, t):
# Single blob advected by u... |
95d414c64f557a25b91e08d1f1c47e210d2dab03c4d90bf4bfa1dc1571898613 | Python | 8,050 | 179 | """The committed training regression set is what it claims to be.
``datasets/regression_train.xyz`` is the dataset the legacy-versus-rewrite
training comparison runs on, and it is committed, so nothing regenerates it
between runs -- which means nothing would notice if it drifted, went stale
against its own recipe, or ... |
e14f3d45352069984489c254950185613dd625cfcd9604f67b1a8a5b0d1adfb4 | Python | 8,054 | 272 | # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
"""
Helpers for parsing protein structure files and generating contact maps.
"""
import gzip
import boto3
import numpy as np
import pandas as pd
from io import StringIO
from Bio.PDB.Polypeptide import three_to_one, i... |
2371b95e0a789bb624bfef872f57004550c3e5332be451885309d2b61073411f | Python | 8,056 | 159 | """Synthetic release checks, without private assay rows."""
import importlib.util
import os
import subprocess
import sys
from pathlib import Path
import numpy as np
import polars as pl
import pytest
from vdjdb.score.pipeline import load_model
def test_v32_default_and_both_legacy_versions():
model, _ = load_mode... |
7e8e0738ce969e7dfd51751eaabe7dcc739f5ca4fb48a8239c4a3b8ef890db6d | Python | 8,057 | 246 | import argparse
import json
import os
import time
import warnings
import numpy as np
from pydfc import data_loader, multi_analysis_utils
warnings.simplefilter("ignore")
os.environ["MKL_NUM_THREADS"] = "16"
os.environ["NUMEXPR_NUM_THREADS"] = "16"
os.environ["OMP_NUM_THREADS"] = "16"
###############################... |
fc311836948aa02d8fd1362d9b553be281186c9b1a03cb26867253c38961415b | Python | 8,057 | 236 | """Input validation for `BrainData`.
Helpers that validate constructor inputs, array shapes, and operand
compatibility between `BrainData` objects and other data types.
"""
from pathlib import Path
import nibabel as nib
import numpy as np
def _validate_brain_data_shapes(brain1, brain2, operation="operation"):
... |
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