sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
16786510e203cbe1bda200d3f877e304cc40686edbec3ca6068d1f16ea58d990 | Python | 1,625 | 42 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
cf22adf1f7786c67cb1354819f01100bff68ed7283ac310de7e1fd3ff5d98e22 | Python | 1,625 | 57 | import argparse
from pathlib import Path
import torch
def convert_weights(weight):
"""Weight Converter.
Converts the weights from timm to mmcls
Args:
weight (dict): weight dict from timm
Returns: converted weight dict for mmcls
"""
result = dict()
result['meta'] = dict()
te... |
49c02a1efd17afeeaf1103feed6aee949005119416ab3c1a0b89e524f2f01a35 | Python | 1,626 | 50 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
class CenterCropPad(OpRun):
def _run(self, input_data, shape, axes=None):
axes = axes or self.axes
input_rank = len(input... |
2176efc0965f3bb68c32fc4a69d1a73d25162202b3031911925b54691a82eeb1 | Python | 1,627 | 40 | import matplotlib.pyplot as plt
import numpy as np
from neuron import h
def plot(x, y, xlabel, ylabel, title, filename):
plt.plot(x, y)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title)
plt.savefig(filename)
plt.show()
name_of_sim = 'youngPN'
target_path = './Results/' + name_of_sim
so... |
bdf4f093b9f3be150fd36f82567fb4f8e9a7269c8e856c48bb88043acea0c281 | Python | 1,628 | 48 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Unit tests for (dunder) composition functionality attached to the base class."""
import numpy as np
import pytest
from sktime.classification.compose import MultiplexClassifier
from sktime.classification.dummy import DummyClassifier
from sktime... |
89b71ffd6aff1f671efe1bddad56c8a020fa2943483e565ec94e87eda6271f3c | Python | 1,630 | 64 | #!/usr/bin/env python3
# CBDA validation and training set creation.
# This script lists the contents of the Pickle file containing the validation
# ordinals, etc.
import sys
import argparse
import os
import pickle
def defineArgs(args=None):
parser = argparse.ArgumentParser()
msg = 'The file name of the Pi... |
d09dbb115a0432c1bd3459668d8d5db6a388343acb25f7e8acb398d591d4a01b | Python | 1,630 | 45 | from setuptools import setup
setup(
name='colorednoise',
version='2.2.0',
description='Generate Gaussian (1/f)**beta noise (e.g. pink noise)',
long_description="""Generate Gaussian distributed noise with a power law spectrum.
Based on the algorithm in
Timmer, J. and Koenig, M.:
... |
297fad411b643c1805c850150fea1b7e16c922c169b024dc96f73bec75aa2964 | Python | 1,632 | 55 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Isolated Python reference calculations for native LAMMPS tests."""
import json
import subprocess
import sys
import tempfile
from pathlib import (
Path,
)
from typing import (
Any,
)
def run_python_reference(script: str) -> Any:
"""Run a reference calculatio... |
3410d4f6a201c0b165160f66a3afc90a029b5d4d11ad0afb71493a6ad7b7af2a | Python | 1,632 | 56 | ###############################################################################
# DoC Stage 4 but with a fake mouse
###############################################################################
from camstim.change import DoCTask, DoCImageStimulus, DoCTrialGenerator
from camstim.automation import PerfectDoCMouse, Stu... |
64a2aa638b0036a68bed22556a0afa3fee9b97644ac40e3e661312f2983091fb | Python | 1,632 | 42 | r"""
An interactive python script that lets you change the save location of datasets,
models and logs to wherever you want them to be (also migrates existing data).
"""
from pathlib import Path
import json
import shutil
from vp_suite.utils.utils import timed_input
from vp_suite.defaults import SETTINGS
if __name__ =... |
7d0c89f2e43d839fd442641980390bdbc0215cb2221100d5c78529e50b22a2bc | Python | 1,633 | 48 | import os
from keras.models import load_model
import numpy as np
import scipy as sp
def load_all_models(config, model_string=''):
models_dir = f'tl_models/transfer_learning/{config.tl_data}/set{config.set}/{config.train_type}/'
all_models = []
model_ind = 0
model_path = models_dir + 'model... |
f5cef99484b1b03dbad188b34382d55613a85b5f364b095a062032f70f83126e | Python | 1,633 | 52 | import torch
import torch.nn as nn
from .cnn1d import CNN1d
class ARModel(nn.Module):
def __init__(self, n_channels: int, n_feats: int, cnn_hparams: dict):
super().__init__()
self.convs = CNN1d(n_channels=n_channels, n_out=45, **cnn_hparams)
self.feat_encoder = nn.Sequential(
... |
1a19243d3f70208167f3008229f7542dac473114808cbb387a5e98a52695ed9a | Python | 1,634 | 57 | """A simple script to extract the colors of the rects in an svg-file.
"""
import json
import re
import xml.dom.minidom
import numpy as np
PALETTE_SVG_IN = "palette.svg"
PALETTE_JSON_OUT = "palette.json"
RECT_DTYPE = [("x", float), ("y", float), ("fill", "U7")]
NAME_DTYPE = [("x", float), ("y", float), ("name", "U15... |
4e719fe43f044b27da8e83ac5a52cc4706c8520886639b0214d70b22123ef32d | Python | 1,634 | 50 | # Mocapy: A parallelized Dynamic Bayesian Network toolkit
#
# Copyright (C) 2004 Thomas Hamelryck
#
# This library is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License... |
6dfc6d59080f86995a78b14fa4ace9c29d0d57738ac0e6a64156fd63a0f936c9 | Python | 1,634 | 51 | #!/usr/bin/env python
from __future__ import print_function
import sys,os
import re
import argparse
import logging
desc = 'Converting "contigs_report_contigs_filtered.mis_contigs.info" to a tsv table'
epi = """DESCRIPTION:
Only mis-assembly contigs will be included.
Output table columns:
*) contig ID
*) misassembly t... |
5739fddfc458d00b0ead8f5cb1400147806ca494c2f62d5b528998abce4565da | Python | 1,635 | 62 | from __future__ import division
import os
import sys
import pandas as pd
#################################
args = sys.argv[1:]
if len(args) > 0:
path = args[0]
if path != 'test':
if not path.endswith('/'):
path += '/'
path += 'output/'
surface_stat = pd.DataFrame()
... |
61eaf404ae66254e01d00e29aa796102ca00fcb959f20fbd92ec35f5511862ea | Python | 1,636 | 64 | # coding=utf-8
# 2021.03 modified (1) replace tensorflow with pytorch
# 2021.03 deleted (1) glob, plt;
# (2) get_init_path, count_accuracy, plot_solution
# Huawei Technologies Co., Ltd.
#
# Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#
# Copyright (c) Ignavier Ng (https:... |
9a5d6260fe474e7f095e63ee40f7dc8d74506ff285f0dcdee14ccad6fa2e8537 | Python | 1,636 | 49 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
2a4e577de4f3721e4148604656ef5c1dc913cbce6bd4291ad9a8caa92cb9d8da | Python | 1,638 | 57 | ###############################################################################
# DoC Stage 1
###############################################################################
from camstim.change import DoCTask, DoCStimulus, DoCTrialGenerator
from camstim import Window, Experiment
from psychopy import visual
import logg... |
4371489b00a889f8ecb591c880adf4736f87ff1299f2881f3fd6124ba4fc7174 | Python | 1,638 | 41 | import time
from connect_laser_device import connect_laser_device
class ConnectionCheckClient:
# def __init__(self, host, port):
def __init__(self):
# 出力デバイスとの接続
# self.connected2serialClient = False
# print('in __init__ of classifierClient, self.connected2serialClient = False')
... |
a7c08e733927f0a128f6c73c22094a5418bc7194e27597139583d25b80eec85b | Python | 1,639 | 48 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
ef21888b51345af7ccbfc00716501cb57ffa65258d14fe36015e77b6d7ba7842 | Python | 1,640 | 52 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
from onnx.numpy_helper import create_random_int
class BitwiseOr(Base):
@... |
04c681867ad9b88d874f0a10585b25959a8cde799f9e9cd5ee4f3c1543f4c946 | Python | 1,641 | 57 | import dolfin as df
from .model_base import ModelBase
class Model(ModelBase):
""" Problem with input zone in the middle. """
def __init__(self, mesh, L, t_PDE, j_in_const, stim_start, stim_end):
ModelBase.__init__(self, mesh, L, t_PDE)
self.stim_start = stim_start # time of input onset (s)
... |
739f1d199ead5a4402cfe6e6e18842c2d8b60ca19d34b131994935c4ab2ca064 | Python | 1,641 | 59 | """Default models for ParaDime.
The :mod:`paradime.models` module implements default models for several
applications, such as a simple
:class:`paradime.models.FullyConnectedEmbeddingModel`.
"""
import torch
class Model(torch.nn.Module):
"""A placeholder model that lists all methods used by the losses defined
... |
fbaa499eb27cafcf10976d7bb16f907f12a7f8a4fc0adcac5934f3eb515a2021 | Python | 1,641 | 54 | """Dummy anomaly detector which detects no anomalies."""
from sktime.detection.base import BaseDetector
class ZeroAnomalies(BaseDetector):
"""Dummy anomaly detector which detects no anomalies ever.
Naive method that can serve as benchmarking pipeline or API test.
Detects no anomalies.
Examples
... |
212d6fff885b1458966246f3d4da8e7ae5eafd4fba4c207fe5f648996b9171a9 | Python | 1,642 | 45 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
0d45dc70dffd940013b6e4434a443bd131b4f710d6e5a6314aef58d63a024dd4 | Python | 1,643 | 70 | #!/usr/bin/env python3
"""Generate slim ontology files
Usage:
slimgen [options] (chebi|gene|doid)...
slimgen [options] all
Options:
-h --help show this
-j --jobs=NJOBS number of jobs [default: 1]
-d --debug
"""
from pyontutils import clifun as clif
import nifstd_tools.chebi_slim
... |
7d6e79150b483a94419976df082350e6b41c3599c2de789069d7ffe4df8e7c0f | Python | 1,644 | 56 | ###############################################################################
# DoC Stage 2
###############################################################################
from camstim.change import DoCTask, DoCStimulus, DoCTrialGenerator
from camstim import Window, Experiment
from psychopy import visual
import logg... |
b308f46c3743d6f827bac4766cafba03120382b90e649188ad253c60e9f60061 | Python | 1,644 | 49 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
2fd92b97cf960bc6e5cd10570a6798b4aec3a149a18ae7ca73c3c0e0d6cf33e5 | Python | 1,645 | 47 | """Tests for detection output converters."""
import pandas as pd
import pytest
from sktime.detection._datatypes._convert import (
_convert_points_to_segments,
_convert_segments_to_points,
)
from sktime.detection._datatypes._examples import (
_get_example_points_2,
_get_example_points_3,
_get_examp... |
ca73af32af322dd912d1ad0e9b695fa904f4fa669f693043b67413f8f4b4652b | Python | 1,645 | 55 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
class GlobalMaxPool(Base):
@staticmethod
def export() -> None:
... |
08f496be2b9fd08f7375a6362fb6d3308c332cd8124c5de636bdf355d01435f3 | Python | 1,646 | 45 | #%%
import ast
import json
from glob import glob
import nbformat as nbf
# Collect a list of all notebooks in the content folder
loc = "bilateral-connectome/docs/**/*.ipynb"
notebooks = glob(loc, recursive=True)
# HACK what is the globby way to do this?
notebooks = [n for n in notebooks if "_build" not in n]
data_ke... |
e0b12cf2118fb2eb50be5764f88080890b9a50872c9532ccccac57920e824ce8 | Python | 1,646 | 52 | from keras.models import load_model
import os
import numpy as np
import scipy as sp
def load_all_models(config):
models_dir = f'models/transfer_learning/{config.tl_data}/set{config.set}/{config.pre_train_data}/{config.enzyme}/{config.train_type}/'
all_models = []
model_ind = 0
model_pa... |
8006bf31cc1234f45425a73670f91abc32c6d8d836df30bac41960315001b4da | Python | 1,647 | 48 | import numpy as np
import sys
from parameterSetup import ParameterSetup
from evaluationCriteria import y2sensitivity, y2confusionMat, printConfusionMat, mathewsCorrelationCoefficient, multiClassMCC
args = sys.argv
params = ParameterSetup()
predFileName = args[1]
testFilePath = args[2]
y_pred = []
with open(params.pre... |
8a97009eea15ea1a13bf3f07994a08a797af4dc126c8c6ac992eef93751e09f2 | Python | 1,647 | 50 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops._op import OpRunReduceNumpy
class ReduceMin_1(OpRunReduceNumpy):
def _run(self, data, axes=None, keepdims=None):
axes = tuple(axes) if axes is no... |
5706bb9e2b60989fb7f258e8e3471fce182449948ca9d22ceec15859a1b8edf4 | Python | 1,649 | 53 | #!/usr/bin/env python
# coding: utf-8
import argparse
import os
import pandas as pd
from atom3d.util import file as fi
def get_label(pdb, label_df):
return label_df[label_df['pdb'] == pdb]['label'].iloc[0]
def main(datapath, out_path):
valid_pdbs = [fi.get_pdb_code(f) for f in fi.find_files(out_path, 'sdf... |
b63152c9231cbd7b4af208cc3ac57dc26aa62cd64e368dcd2fb60691c5f2f190 | Python | 1,650 | 51 | # Copyright (c) OpenMMLab. All rights reserved.
import base64
import os
import mmcv
import torch
from ts.torch_handler.base_handler import BaseHandler
from mmcls.apis import inference_model, init_model
class MMclsHandler(BaseHandler):
def initialize(self, context):
properties = context.system_propertie... |
d6111e46d604acd667f307100a85edeecdab1a0967b9493663c50d56fdf1a35a | Python | 1,653 | 57 | ###############################################################################
# DoC Stage 4 but with a fake mouse
###############################################################################
from camstim.change import DoCTask, DoCImageStimulus, DoCTrialGenerator
from camstim.automation import PerfectDoCMouse, Stu... |
9ac783e2659c63a9349365b1b4d7e8bce1e3b7287eac157076141694829c4c13 | Python | 1,657 | 44 | # Copyright 2022 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
cad484d17239cfe63c60fe271df52ae5f67926be7f079aadec62a4b65a8cffa6 | Python | 1,657 | 64 | import torch
import torch.nn as nn
from PIL import Image
from torch.utils.data import Dataset
class FusionModel(nn.Module):
def __init__(self, encoder):
super(FusionModel, self).__init__()
self.encoder = encoder
self.encoder.fc = nn.Identity()
self.fusion = nn.Sequential(
... |
8f0d5efbf4f38d657eb3c656bbb8cd7fdfe5f95b20cb4798279cec9091603866 | Python | 1,659 | 60 | import os
import pytest
from asreview import ASReviewData
from asreview.models.feature_extraction import get_feature_model
from asreview.models.feature_extraction import list_feature_extraction
ADVANCED_DEPS = {"tensorflow": False}
REQUIRES_EXTRA_DEPS = ["doc2vec", "embedding-idf", "sbert"]
try:
import tensorf... |
d92a7a4c88dfff19f2ee82d7ac6ec1d62b39cee2d781442097ce977be8d5566c | Python | 1,659 | 48 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
48857e6c6787a8a208cc3276fc54a6e3e1ee5b659c16c0364dc0640968a4ccaa | Python | 1,660 | 51 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
4b5879f31ce72fca58ad5dff8389dc8f38b2d1d9b8f63fadc0f965c441f47156 | Python | 1,660 | 45 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
352fdc618ef398b086b92bb37ee50887c7ec625ca4e6b856c8f87c4e5f7aab44 | Python | 1,662 | 77 | import torch
import torch.nn as nn
from lgn.g_lib import GTau
class NoLayer(nn.Module):
"""
Layer that does nothing in the LGN architecture.
This exists just to demonstrate the structure one would want if edge
features were desired at the input/output.
"""
def __init__(self, *args, **kwargs... |
339561b287880efb2bb0f595a1cec2e3be055a389afaef50657b49e128eda848 | Python | 1,664 | 46 | # Copyright 2022 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
3caca56ddbdbad82ef6d71d78fa23b6a137e6657e36fce20de0354acb89f0cd8 | Python | 1,664 | 56 | import unittest
import numpy as np
from ddt import ddt, data
import SPHARM.lib.transformation as tr
@ddt
class TestTransformation(unittest.TestCase):
@data(
([2, 908, -234, 0.3], [654, -6, -64, 2], [-32, 243, 24, -22]),
)
def test_spherical_transform(self, coords):
x, y, z = coords
... |
4ffe84fcf5188bd9ec687227bd6991d15019c01593fc6d8b212db1e6e8f50852 | Python | 1,664 | 34 | '''
Pure-python implementation of UCSC "liftover" genome coordinate conversion.
Copyright 2013, Konstantin Tretyakov.
http://kt.era.ee/
Licensed under MIT license.
PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.
It uses the same logic and coordinate... |
ed00b8aa8d996be0a4a680e428fff2ab3d18896f69ceda30fdcf64c20e2804b3 | Python | 1,664 | 48 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
c0008fa7e89aece8613002f59c1601357530262e2f37bdaf6893f986f7dc428a | Python | 1,666 | 54 | """
Palantir - Modeling continuous cell state and cell fate choices in single cell data.
Palantir is an algorithm to align cells along differentiation trajectories, identify
differentiation endpoints, and estimate cell-fate probabilities in single-cell data.
The package provides functions for preprocessing, visualizat... |
243142504dc20eab2f2cbc36f4865fcdd84c77ffd33702476a60fc4a0819ee97 | Python | 1,667 | 73 | #!/usr/bin/python
"""
test and plot hcno stuff
"""
import numpy as np
import matplotlib.pyplot as plt
#Parameters#
gbar = 0.0005 # (mho/cm2)
vhalf1 = -50 # (mV) # v 1/2 for forward
vhalf2 = -84 # (mV) # v 1/2 for backward
gm1 = 0.3 ## (mV) # sl... |
ec1ed268f32e57307330768ab0d4819a59a06daf05f92374076856bc2fc1b8e6 | Python | 1,668 | 55 | # Copyright (c) OpenMMLab. All rights reserved.
try:
import timm
except ImportError:
timm = None
from ..builder import BACKBONES
from .base_backbone import BaseBackbone
@BACKBONES.register_module()
class TIMMBackbone(BaseBackbone):
"""Wrapper to use backbones from timm library. More details can be found ... |
38015794acfcac146a3d2e54ee8aeaeee526105fccd8ae93e6fc02c54e425e0a | Python | 1,672 | 55 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
from onnx.numpy_helper import create_random_int
class BitwiseXor(Base):
... |
8d15f766a8a17672c63394f5f938a3cdcf2612b0bb68e8800a828a5dc8a5948e | Python | 1,672 | 40 | # Copyright 2023 The TensorFlow 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 applica... |
a60187acd032b219eac3d014c2570c8a2f8f498b7bad694964c1015b2060a8a7 | Python | 1,672 | 53 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import ml_dtypes
import numpy as np
import pytest
from numpy.testing import assert_allclose
from onnx.helper import make_node
from onnx.reference import ReferenceEvaluator
class TestReferenceEvaluatorD... |
1816afdb35aec6af8a62a6478fbb5bcab0bfa6d929992c4545ca945e74378d48 | Python | 1,673 | 71 | from __future__ import annotations
from numpy import log as nlog
from pandas import SparseDtype
from .STDataset import STDataset
def cpm_normalizer(dataset: STDataset) -> STDataset:
"""
Perform CPM on dataset.
Parameters
==========
dataset : STDataset
STDataset to be normalized.
Re... |
c5a3faf2449ac7c00683ba08fce75ab747983c2e2f4ec0816ee39ab6d057c010 | Python | 1,673 | 55 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
from onnx.numpy_helper import create_random_int
class BitwiseAnd(Base):
... |
f57e2c0066e4ccd58069b7f6cdc3092152873bcaf078b9d98adc54f1cb7d5482 | Python | 1,673 | 50 | # Copyright 2022 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
41a1316ef420b5bc2fe0a3cef09e92d91655accc8472676ab798023ea9688f45 | Python | 1,674 | 56 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
931210a84f556c4045af5cc750e41cdb28fd3a975f6c06ae7154a055cf286e9a | Python | 1,674 | 57 | # Copyright (c) OpenMMLab. All rights reserved.
from abc import ABCMeta, abstractmethod
import numpy as np
import torch
import torch.nn.functional as F
from .builder import AUGMENT
class BaseMixupLayer(object, metaclass=ABCMeta):
"""Base class for MixupLayer.
Args:
alpha (float): Parameters for Bet... |
a2fb6706132459ad716d1fd8692be85e119d6751ae6cacd2e71a694ddbafb6ce | Python | 1,674 | 48 | import numpy as np
import math
from scipy.signal import butter, lfilter
def butter_bandpass(lowcut, highcut, fs, order=1):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
b, a = butter(order, [low, high], btype='band')
return b, a
def butter_bandpass_filter(data, lowcut, highcut, fs, order... |
b0bc825f88cf541193bc9d46b7259fb5b92ed2b5b56636df544c877bd254e506 | Python | 1,674 | 49 | from sciunit.models.backends import Backend
import time
class NestBackend(Backend):
name = 'Nest'
nest_instance = None
def init_backend(self, **kwargs):
print("Initialize {} backend".format(self.name))
# print("Nest version: {}".format(nest.version()))
print("Use memory chache: {}... |
d1f8e2108c89b7c6a3d867f64704d42d4dcbc38ddf343b4784a2e90bf02f6afc | Python | 1,674 | 55 |
# pylint: disable=missing-docstring
import json
class Model(object):
"""
Model is a part of the manifest.json. It defines the properties of the model such as name, version as weill
as the entry point into the service code through the handler property
"""
def __init__(self, model_name, serialize... |
fc5dd6d76c9e4faeebcf8d548df6f9d5f13f70610d7ccf6c5d51094af1e48cc4 | Python | 1,674 | 63 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import pytest
pytest.importorskip("sphinx")
from docs.docsgen.source import onnx_sphinx
@pytest.mark.parametrize(
"op_name",
[
"BatchNormalization",
"GreaterOrEqual",
... |
7273f8003921ec4a89a5e510d9b2b1d58139951849cc786da7d5c721247859ee | Python | 1,677 | 70 | #%%
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from pkg.data import load_split_connectome
from pkg.io import OUT_PATH
from pkg.io import glue as default_glue
from pkg.io import savefig
from pkg.utils import get_hemisphere_indices
from graspologic.match import graph_match
FILENAME = "maggo... |
72f69f16fee94b4967f2f0ff272192286395400fb0f314623a54a65b7fc892ce | Python | 1,679 | 58 | """Clustering averaging metrics."""
__author__ = ["chrisholder", "TonyBagnall"]
from collections.abc import Callable
import numpy as np
from sktime.clustering.metrics.averaging._dba import dba
def mean_average(X: np.ndarray, **kwargs) -> np.ndarray:
"""Compute the mean average of time series.
Parameters
... |
298df4f0263a894e0ed79f5653697d1c69ab37b6c8188006dce5e5d180d90a2d | Python | 1,680 | 50 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
eb9d79d09825ca2f137c425c1ccd5a903eda0799538dabae430386e665bad7a3 | Python | 1,681 | 54 | """Module for the configuration of how and what is recorded in the log file."""
import sys
import logging
import warnings
def log_exception(exc_type, exc_value, exc_tb):
"""Sets up the recording of exceptions on the log file
@param exc_type: Type of exception
@param exc_value: Value of the exception
... |
f7e6d21f1fd71d096521a0904e31ea37ef12b819200ecbc6d3cfa608b9adf334 | Python | 1,681 | 50 | """Tests for DistFromAligner symmetry."""
import numpy as np
import pytest
from sktime.alignment.lucky import AlignerLuckyDtw
from sktime.datasets import load_unit_test
from sktime.dists_kernels.compose_from_align import DistFromAligner
from sktime.tests.test_switch import run_test_for_class
@pytest.mark.skipif(
... |
ae23104d18cd9ea3bdb6eb7a218b654f75019060f0b1b210ffefe1025cb0cd9e | Python | 1,684 | 53 | #!/usr/bin/env python3
import csv
from io import StringIO
import rdflib
import requests
from pyontutils.utils import rowParse
from pyontutils.core import makePrefixes, makeGraph
from pyontutils.namespaces import makePrefixes, TEMP
try:
breakpoint
except NameError:
from IPython import embed as breakpoint
def m... |
47aa3b6bf2c228f717688ff097cb8ea22da32c994edc5b23b903717f7f6e7cd4 | Python | 1,685 | 47 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops._op import OpRunReduceNumpy
class ReduceMax_1(OpRunReduceNumpy):
def _run(self, data, axes=None, keepdims=None):
axes = tuple(axes) if axes is no... |
51c8fbf278f24b802d3cadf8789ce2feed41e99ae57bf9ee2d4301fa61473d3b | Python | 1,685 | 39 | import matplotlib
matplotlib.rcParams["figure.dpi"] = 100
matplotlib.rcParams["image.cmap"] = "Spectral_r"
matplotlib.rcParams["axes.spines.bottom"] = "on"
matplotlib.rcParams["axes.spines.top"] = "off"
matplotlib.rcParams["axes.spines.left"] = "on"
matplotlib.rcParams["axes.spines.right"] = "off"
matplotlib.rcParams[... |
53b2bf62d7bd5d9ac3a4a6ac855b9b2e30c14a84aeac9231a00aed8528d60004 | Python | 1,685 | 48 | import torch
from base.proposer_base import Proposer
from gln.test.model_inference import RetroGLN
from typing import Dict, List
class GLNProposer(Proposer):
"""GLN proposer, wrapping around gln.test.model_inference.RetroGLN"""
def __init__(self,
model_name: str,
model_args,... |
9b80300536eab7ffb2a022852b150237fa23975a631e394dd3f1599a1bff48a5 | Python | 1,686 | 53 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
c7f673b962d62b39066e3a3c255064a046748022d6a85f91befa0ba316d1f365 | Python | 1,687 | 69 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""The atomic model provides the prediction of some property on each
atom. All the atomic models are not supposed to be directly accessed
by users, but it provides a convenient interface for the
implementation of models.
Taking the energy models for example, the developere... |
09ddee4ef44fb12bc289455272d9a218d0a1ef699b3186fe48215738bd42607f | Python | 1,692 | 60 | # Copyright 2026 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
b19072c27461d340677defa1aa19bfedbd1a5883bf10536c9fcdd4e9e2ccebf1 | Python | 1,692 | 44 | from src.data.process_ephys_data import ephys_mat_to_pkl
import os
# About
# This is a copy of process_m2_ephys_good.py but to process the data
# from recordings in naive mice. The main changes are
# (1) processing active condition is removed
# (2) there is no need to remove active / passive mismatch
# Created: 2021-0... |
03c6b6d916e07a7c92ac4a0ef36e29bea2beca7bc90196bc4b3fd73619b8dbda | Python | 1,693 | 50 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
643ab8efe079d7003b95b78804bee7eb5cb93e28bca32d551a69b836b1ae7e32 | Python | 1,694 | 38 | """Quantile subset for the training loss.
The backbone's native pinball loss is computed over a quantile grid that does not
match the quantiles GIFT-Eval actually scores. PatchTST-FM predicts 99 quantiles,
while only 9 of them (0.1 .. 0.9) enter the score, so 90 quantiles receive gradient
without ever affecting the me... |
55f305f6563ca11dab6e7c7aa7fbb2df68c7f71b7cd39934bd417237c363fc18 | Python | 1,695 | 66 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
5eb679617969f97eef7e164f832252452c35f19e1c864ba7e8fea9cc86ad7a90 | Python | 1,695 | 46 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
_acceptable_str_dtypes = ("U", "O")
def pad_empty_string(
split_lists: list | np.ndarray, padding_requirement: list | int
) -> list:
... |
b9b22e354d333cd9f6c368762e2548f7845c4a6b2b20c5eb8ba223ffc139ffc0 | Python | 1,695 | 40 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
from setuptools import setup, find_packages
from ampligraph import __version__ ... |
603c8597738387e6da5dfa5066cdd0e5828ad4ec47fe84b69a8c991584da5b9a | Python | 1,697 | 50 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
787b1b8d725dbb8bdc7eb6ec99ffd154c8d26d16e27c8d2f184cab86667cf803 | Python | 1,697 | 64 | from scipy.sparse import find, csr_matrix
import pytest
import pandas as pd
import scanpy as sc
import numpy as np
from palantir.utils import compute_kernel
@pytest.fixture
def mock_data():
n_cells = 50
n_genes = 10
rng = np.random.default_rng()
return pd.DataFrame(
rng.random((n_cells, n_gen... |
8fa6f2f450cb9d6a53c37db450871187411733357a1471a22ddf159ce03ede9e | Python | 1,697 | 40 | import torch
import torch.nn as nn
import torch.nn.functional as F
class MLP(nn.Module):
"""A basic feed-forward neural network (MLP), with tunable hidden layer number and dimension.
The number of layers is assumed to be equal to :math:`len(hidden\_dims) + 2`, including the input and output layers.
... |
9530343f7f963c0dbea18cbe6f8e2e2c5dda353f3f0000ac86853bdda2f6b6b7 | Python | 1,698 | 58 | """To compile and install locally run "python setup.py build_ext --inplace".
To install library to Python site-packages run "python -m pip install --use-feature=in-tree-build ."
"""
import platform
import sys
import sysconfig
from pathlib import Path
from setuptools import setup, Extension
import numpy as np
from Cyth... |
72909bff17c4e3c8e952f9412ac2d92e3cd29793516e13ec1729335a6f196a58 | Python | 1,699 | 51 | from netplotbrain import plot as npbplot
import pytest
import pandas as pd
import numpy as np
# Example node and edges dataframes included with package
nodes = pd.read_csv('./examples/example_nodes.tsv', sep='\t', index_col=0)
edges = pd.read_csv('./examples/example_edges.tsv', sep='\t', index_col=0)
# Create an edge... |
bec75c028f22a51d37bb09a2594ecb65fc795b15b26e7a9486a7bdb86337fa53 | Python | 1,699 | 51 | """Tests for bycycle.cyclepoints.extrema."""
import pytest
import numpy as np
from scipy.signal import argrelextrema
from bycycle.tests.tsettings import FS, F_RANGE
from bycycle.cyclepoints.extrema import *
###################################################################################################
########... |
0e83315600d207e33190caa03e74f30fa3aca75b51155f2a91ba4f73de546cb0 | Python | 1,700 | 48 | # Copyright 2019 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
0ddd57fe1e91437298d846e17a9ca1ff60c9cf3e5aa2117f6fcd34a98872ec71 | Python | 1,701 | 58 | from __future__ import division
import torch
import torch.nn as nn
class Sparsemax(nn.Module):
def __init__(self, dim=None):
super(Sparsemax, self).__init__()
self.dim = -1 if dim is None else dim
def forward(self, input):
input = input.transpose(0, self.dim)
original_size... |
7b935840f88888ffea799583d800ed92910f22e1faa1d0bd1e6322f842c5149a | Python | 1,701 | 50 | import os
import numpy as np
import pandas as pd
def writeToFile(authors, features, author2id, paper_ids, content):
""" Writes all data into files
The following files are written
- dataset/features.csv
- dataset/authors.txt
- dataset/paper_ids.csv
- dataset/author2id.csv
- dataset/content.c... |
d40b37f850c9286c3c7ac8e245ff1dcde37893c062046901e282fa2bf51614e2 | Python | 1,701 | 57 | import os
import numpy as np
# Read in all files and split them according to the specification.
with open("dataset/content.csv") as f:
content = f.read().strip("\n").split("\n")
with open("dataset/features.csv") as f:
features = f.read().strip("\n").split("\n")
with open("dataset/paper_ids.csv") as f:
pa... |
95a337d32067bb8b6b5ab67f34f44af6b3f1290c9401f11dfcedd127085f809c | Python | 1,703 | 44 | import qt, ctk, slicer
from AbstractScriptedSubjectHierarchyPlugin import *
class ElastixPresetSubjectHierarchyPlugin(AbstractScriptedSubjectHierarchyPlugin):
# Necessary static member to be able to set python source to scripted subject hierarchy plugin
filePath = __file__
def __init__(self, scriptedPlugin):
... |
ab3d0315b28658c47679be8dd518b6c1360bec1e8ae95d7444507432bf9b6a3c | Python | 1,703 | 47 | """
Test the ccstim generator.
Usage: python test_ccstim.py
This script runs ccstim for each of it's potential inputs, and plots the resulting waveforms.
"""
import sys
import numpy as np
from cnmodel.util import ccstim
import pyqtgraph as pg
pulsetypes = ['square', 'hyp', 'timedSpikes', 'exp']
def test_cc_stim(... |
c633d09bf9418d146f1140a9bf9fa0caee51c1262a781dca9b672eb6272af874 | Python | 1,703 | 49 | # coding=utf-8
# Copyright (C) 2022. Huawei Technologies Co., Ltd. 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
#
# ... |
95b72e7eba29335f9022eaf0a59ace358d32eb64e3d70b3ada44feb97b544d8b | Python | 1,705 | 46 | #-------------------------------------------------------------------------------
# elftools example: elf_notes.py
#
# An example of obtaining note sections from an ELF file and examining
# the notes it contains.
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#----------------------------------... |
ba3ccaca4b8eafb294438378269c8aea985d7a9f6bdd7ecd26f7c6ccbf56fef8 | Python | 1,705 | 48 | # Copyright 2019 The TensorFlow 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 applica... |
d4352faa34671ac38bdda58c11d656096c5e0b1fd7ea313fcbbeb1258a007bb2 | Python | 1,705 | 59 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmcv.utils import digit_version
from mmcls.models.utils import channel_shuffle, is_tracing, make_divisible
def test_make_divisible():
# test min_value is None
result = make_divisible(34, 8, None)
assert result == 32
# te... |
d72958f02ba44230b3c190a58bebc789fdc21fa3ca58f42a5c9faf91ceb04c4d | Python | 1,705 | 50 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. 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
#
# ... |
0475b98445f7cd6980e7fd6135c19e8ca3b1717269ac7c64007809c5000910e7 | Python | 1,706 | 59 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
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