sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fe15018b2b138b2f842d8eb9606b41c2ac5f1b135c4ddfcf2085cdf4ecbce6ff | Python | 2,289 | 56 | from __future__ import print_function
import numpy as np
from itertools import groupby
from featureExtractor import FeatureExtractor
class FeatureExtractorFreqHisto(FeatureExtractor):
def __init__(self, params):
self.params = params
self.extractorType = 'freqHisto'
def getFeatures(self, eegSe... |
d91f060110567615de121f0f423bee9890cf24503bf4c6743aaf7142c4866045 | Python | 2,291 | 77 | import cv2
import matplotlib.pyplot as plt
import numpy as np
import pdb
from scipy.signal import find_peaks
def peaker(data):
peaks,_ = find_peaks(data,prominence=0.5)
peakDist = np.mean(np.diff(peaks)) /2
# peaks, _ = find_peaks(data,distance=peakDist)
peaks = [0] + list(peaks) + [len(data)-1]
ret... |
be365120fe0c548b820d24cefdfa225d9a4946341f233e44e8244c9c7664b6a7 | Python | 2,292 | 80 | # 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
def swiglu(a: np.ndarray, b: np.ndarray, alpha: float) -> np.ndarray:
sw... |
37e9eee0ad0d19cafc98855116e579f16182d93bbad5de2438bbe190bb79c192 | Python | 2,293 | 48 | """Script for the direct comparison of the GNN performance compared to DFT."""
import argparse
import sys
sys.path.insert(0, "../src")
import matplotlib.pyplot as plt
from gnn_eads.functions import get_graph_sample
from gnn_eads.graph_tools import visualize_graph
from gnn_eads.nets import PreTrainedModel
if __name_... |
4736c4cd1eedaa85475ea589bc899bd60b9d6563aa6944bb88351ac1c2a9392a | Python | 2,295 | 82 | # 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 QLinearConv(Base):
@staticmethod
def export() -> None:
... |
4fa756e8c47739efea2feb79444f2e5be655f0357c5f6df571e61e452404d70c | Python | 2,296 | 62 | #-------------------------------------------------------------------------------
# elftools example: dwarf_die_tree.py
#
# In the .debug_info section, Dwarf Information Entries (DIEs) form a tree.
# pyelftools provides easy access to this tree, as demonstrated here.
#
# Eli Bendersky (eliben@gmail.com)
# This code is i... |
f818556f1589dcb87e8a7a1da4c833a60a483995a5c4262c0622d1e3912289a2 | Python | 2,296 | 71 | from __future__ import division
import numpy as np
import pylab as plt
import os
from helper_lib import filelib
from SPHARM.classes.orbital import Orbital
def test_single_orbitals(gridsize, path):
value = 'amplitude'
filelib.make_folders([path + 'surfaces/', path + 'heatmaps/', path + 'frequencies/'])
f... |
34a94df31b1c8cef424ee7ee3fe4d13389b29ed48afbe6bad4c97d4cb9ce4acc | Python | 2,297 | 65 | """
Modified from torch.utils.data.distributed.DistributedSampler
Support enlarging the dataset for *iter-oriented* training, for saving time when restart the
dataloader after each epoch
"""
import math
import torch
from torch.utils.data.sampler import Sampler
import torch.distributed as dist
class DistIterSampler(Sa... |
57417bd32454ef341d49a29548d16b038e07124924b7cafdbfa683c0a4f41350 | Python | 2,298 | 79 |
# + [markdowmn]
"""
# Tutorial 2: Visualization
### Views
The view is the angle which the brain is viewed from in the plot.
You can specify it as a string:
| Argument | View |
| :-------------: | :----------: |
| 'L' | Left |
| 'R' | Right |
| 'A' | Anterior |
| 'P' | Posterior |
| 'S' ... |
88860a20150c874da9ca33172efcaa1a9a4eb46ba70cb7c40a95e33273383c70 | Python | 2,298 | 87 | # Copyright 2019-2026 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
#
import warnings
class experimentalWarning(Warning):
"""Warning that is tr... |
dd551f0a712e54cc13ee9980bcabc20ef7658e292214f949907d464717e1fbc3 | Python | 2,301 | 83 | # roifile/setup.py
"""Roifile package setuptools script."""
import sys
import re
from setuptools import setup
def search(pattern, code, flags=0):
# return first match for pattern in code
match = re.search(pattern, code, flags)
if match is None:
raise ValueError(f'{pattern!r} not found')
ret... |
69309260016ced9c57a0a21dfe92dfde069c8c8e03041c4f7d0009d350132ac4 | Python | 2,302 | 70 | from pytest import mark
import numpy as np
from asreview.models.classifiers import get_classifier
from asreview.models.query import get_query_model
from asreview.models.query import list_query_strategies
@mark.parametrize("query_strategy", [
"max",
"random",
"max_random",
"uncertainty",
"max_unce... |
73651ded753607e5028136dbd2885380eacb350fbacc890d008ecf5a1f34f9f9 | Python | 2,303 | 82 | import numpy as np
from brian2 import *
# import matplotlib.pyplot as plt
import time
import pickle
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
NEURON AND SYNAPSE DEFINITIONS
"""
globalStart = time.time()
eqs_neuron = '''
dv/dt = (-v+I+Is... |
40c9ab2bcc2bcb59e449bd31f7951564081e54206686ee3aae714308e819695a | Python | 2,304 | 65 | from pathlib import Path
from nltk.translate.bleu_score import sentence_bleu
from statistics import mean
# DIVIDED_BY_THREE_DOTS works well for T2E, and worst for C2E.
DIVIDED_BY_THREE_DOTS = False
if DIVIDED_BY_THREE_DOTS == True:
BASE_DIR = Path("../NMT_input") / Path("tokenization")
TRAIN_INPUT = BASE_DIR ... |
83b1d9adc360e9a74e479b986c3eb5492c8f1f33d98b6c5b192fd0733436655b | Python | 2,304 | 63 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Nov 11 17:21:09 2021
@author: sam
"""
import os
import argparse
from pipeline_utils import submit_job
import glob
from natsort import natsorted
if __name__ == '__main__':
p = argparse.ArgumentParser('Running pipeline on remote', add_help=False)
... |
fc29d0a7014f91fa8e44c5e63481039a902c14fed89744e35f7bc82d36cd2db1 | Python | 2,304 | 76 | import matplotlib.pyplot as plt
import pandas as pd
from rdkit import Chem
from rdkit.Chem import rdChemReactions, rdDepictor, Draw
from rdkit.Chem.Draw import rdMolDraw2D, DrawingOptions
DrawingOptions.atomLabelFontSize = 15
DrawingOptions.dotsPerAngstrom = 100
DrawingOptions.bondLineWidth = 3.0
file = r'C... |
b620463bece42352b744d534ea00e152206c028d038603b3e1ed4a9be27eb5d9 | Python | 2,305 | 77 | # SPDX-License-Identifier: LGPL-3.0-or-later
from collections.abc import (
Callable,
)
from deepmd.dpmodel.descriptor.base_descriptor import (
BaseDescriptor,
)
from deepmd.dpmodel.fitting.base_fitting import (
BaseFitting,
)
from deepmd.utils.data_system import (
DeepmdDataSystem,
)
# use "class" t... |
bee6236f84d50c375e145febe904f4ecf734051cebad252fb593a4b64a810e54 | Python | 2,305 | 58 | # 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... |
3e2df6a5c996bb07eb9a7e92d619a4effb44ad2a8500f090fec6ce2dcdf7720f | Python | 2,306 | 80 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 11 17:56:21 2022
This code identifies and creates pdb files of chains and interacting glycans.
It workd on multi chain pdb files given in a directory.
Note: Input directory has only glycan interacting pdbs.
//
@author: sudhanshu
"""
from mpl_toolk... |
06f5fb0f322b549db46b7485ec479c948ffc202756ef88438620aaf7264c986c | Python | 2,308 | 72 | # 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
#
# ... |
793f1000361cdd11092bbdd82545009931efffec815d5c589f155dc5454f6cc2 | Python | 2,308 | 66 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Tests for BaseObject universal base class that require sktime or sklearn imports."""
__author__ = ["fkiraly"]
def test_get_fitted_params_sklearn():
"""Tests fitted parameter retrieval with sklearn components.
Raises
------
As... |
6614ca0bb6322f0425363c2334ea8b3a6f27a071931e234000195cb2c45bb16b | Python | 2,310 | 79 | from copy import deepcopy
from pathlib import PosixPath
from typing import Optional
import ants
from ants.core.ants_image import ANTsImage
from rich import print
def register(
fixed: ANTsImage,
moving: ANTsImage,
type_of_transform: list,
outprefix: str = "",
path: Optional[PosixPath] = None,
... |
97d988f745750c71f2a8a76bee2e8a93b0754b465550276c40fb8ca4c540e98b | Python | 2,315 | 59 | """Tests for bycycle.features.burst."""
import pytest
import numpy as np
from bycycle.features import *
###################################################################################################
###################################################################################################
@pytest.mar... |
a2cccbc2aca04401f8b3c39f87c244a83282b921c347658fbcbfe7f99a27520a | Python | 2,316 | 59 | #!/usr/bin/env python3
"""Given a ttl file get ILX ids for ILXREPLACE terms.
Usage:
ilxcli [options] <file>...
Options:
-l --logfile=LOG the file mapping ILXREPLACE to ILX [default: ilx-records.json]
-o --ontology=ONT manually set the ontology where ILX identifiers will live
-g --get a... |
e19c0be999fa989d0764fa0a2df5492af1889613b6d8afe9e351501556639f89 | Python | 2,316 | 79 | import unittest
import rdflib
from neurondm.core import (LabelMaker,
Phenotype,
NegPhenotype,
Neuron,
LogicalPhenotype,
AND,
OR,)
class TestLabelMaker(unitt... |
e900bbf932fd52320dc0f590bc98e873b46552efee2f3543e092c91b150b1aa5 | Python | 2,317 | 63 | import argparse
def get_parser():
parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('--action',
type=str,
default=None,
help= 'the simulation to perform.\n new_data requires new_data_path\n ... |
2a98d51b70a9396b54ac592cb5dd0081be21336b3ed98853e4d012ad10dd2ee0 | Python | 2,318 | 63 | '''
import numpy as np
from nibabel import trackvis as tv
from dipy.segment.clustering import QuickBundles
from dipy.io.pickles import save_pickle
from dipy.data import get_data
from dipy.viz import fvtk
fname = get_data('fornix')
streams, hdr = tv.read(fname)
streamlines = [i[0] for i in streams]
qb = QuickBundles(... |
4679bf92d55407cd38f6552161bdd0da41ed7d8bc524a50761409ac70a64d4ea | Python | 2,319 | 64 | import numpy as np
class HyperParam:
def __init__(
self,
min_samp,
max_samp,
init=None,
sample_fn="loguniform",
explore_wt=0.2,
enforce_limits=False,
):
"""Represents constraints on hyperparameter
values that will be used during PBT.
... |
c18b62990c228216dd34e2d6aa1044ebc485f85d9e6ac5d8d6f622fd2a9aed6e | Python | 2,319 | 78 | # Copyright 2019-2020 The ASReview 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 appl... |
109a820335c94a2b253845feefe56a6dfa2e679b273152fad0294b54330c39b4 | Python | 2,320 | 66 | import pickle
import numpy as np
from ksstatistics import StatisticalTester
from fileManagement import readStandardMice, getFileIDs
from parameterSetup import ParameterSetup
eegFilePrefix = 'eegAndStage'
params = ParameterSetup()
pickledDir = params.pickledDir
standardMiceData, standardMiceFileFullNames = readStanda... |
6829d26aaad393fcdcee389bd764c0df687aae3cac97bdbeb22de9f8e861e46e | Python | 2,320 | 72 | # 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... |
921eff397e00249daa9e8858bf65fa9ea1642447246472b83e5577bc3a5eadee | Python | 2,320 | 72 | import pandas as pd
from netplotbrain import plot as npbplot
import pytest
# 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)
@pytest.mark.mpl_image_compare
def... |
a142a9030691a3780ff12a86ac28bea59747e020af41f09fe54a197df48d4a9f | Python | 2,320 | 71 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmcv.utils.parrots_wrapper import _BatchNorm
from mmcls.models.backbones import Res2Net
def check_norm_state(modules, train_state):
"""Check if norm layer is in correct train state."""
for mod in modules:
if isinstance(mo... |
c64bb3e7c66aebcbe255a75616c9c937d8ec0f397726a2003631b41a08db8ffa | Python | 2,320 | 90 | import numpy as np
import matplotlib as mpl
from matplotlib.colors import to_rgb, to_rgba
from numpy.testing import assert_array_equal
USE_PROPS = [
"alpha",
"edgecolor",
"facecolor",
"fill",
"hatch",
"height",
"linestyle",
"linewidth",
"paths",
"xy",
"xydata",
"sizes",... |
427275022d99adac21c114cd38d72df17e2843651be7c89bd586620f3503db23 | Python | 2,322 | 69 | # 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... |
0f522fa56e6b88489c2dccd108c6af462fc3669e9c397adbe8d946350e51c6d2 | Python | 2,324 | 63 | # 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... |
62b2ca93bb40b2e9c74635a78401e28383e4796c99d5ba5f4717d4173f7d4f28 | Python | 2,324 | 86 | #!/usr/bin/env python3
# tifffile/tiff2fsspec.py
"""Write fsspec ReferenceFileSystem for TIFF file.
positional arguments:
tifffile path to the local TIFF input file
url remote URL of TIFF file without file name
optional arguments:
-h, --help show this help message and ... |
57bb273ac5793439455336c68f2bcfa55acc41dc99201eb4743f6235a29e6f11 | Python | 2,325 | 73 | # 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... |
e17fb202631d4ead1686feeda3c23b6d8122cd6101c5e562757f8e85d17fd8e6 | Python | 2,325 | 71 | import json
from urllib.request import urlopen
import requests
from packaging.version import parse
from rich import print as pprint
from hsf import __version__
def get_version(url_pattern: str = 'https://pypi.python.org/pypi/HSF/json'):
"""Returns version of HSF on pypi.python.org using json."""
req = reque... |
218d0e48cc5c411ae3d8366124e630288a03729525461685cf60e8e7916a97d2 | Python | 2,326 | 59 | """ByCycle setup script."""
import os
from setuptools import setup, find_packages
# Get the current version number from inside the module
with open(os.path.join('bycycle', 'version.py')) as version_file:
exec(version_file.read())
# Load the long description from the README
with open('README.rst') as readme_file:... |
96b3db69ba2eb7d5e7a7d87d347a8da6c44dd4b94f701563b795e3610f803b18 | Python | 2,326 | 84 | # Copyright (c) OpenMMLab. All rights reserved.
from copy import deepcopy
import pytest
import torch
from torch.nn.modules import GroupNorm
from torch.nn.modules.batchnorm import _BatchNorm
from mmcls.models.backbones import T2T_ViT
def is_norm(modules):
"""Check if is one of the norms."""
if isinstance(mod... |
4063405f87d90f416785b0a3a50248765ea90a4af30c8b5bcd8f197242a25e63 | Python | 2,327 | 63 | # Copyright 2024 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... |
4e0a91d30e252ec772eb205d9d105166bd6e19641d4eb44a22a0655e6feb4f47 | Python | 2,327 | 73 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
8c29cfd2ae76a020bf681021a274bfd2438cf3b9940c6163ac0270568d5faeee | Python | 2,328 | 65 | """ modulation_transfer_function.py - calculate rate modulation transfer function
Calculates rate modulation transfer function from a spike train, for the specified frequency
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R01 DC015901 (Spirou, Manis, Ellisman),
DC R01 DC004551 (Manis, 2013-... |
999600d18d45df85cc83d23d6341dc8837da005fa1c44b80e18f4898b04fd84b | Python | 2,328 | 60 | from netplotbrain import plot as npbplot
import pytest
import pandas as pd
import matplotlib.pyplot as plt
import templateflow.api as tf
# 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... |
51a38f084a96a46ed914bc7bd586646371c2666f88290b675efd060b1e239cf0 | Python | 2,329 | 47 | # Copyright 2019-2026 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 ampligraph.latent_features.layers.scoring import DistMult
import pytest
... |
e150439c55a208037c109cdc40723b18dfd4c2dfb82a237f98bee5afc34969b0 | Python | 2,329 | 41 | # 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
#
r"""This module includes neural graph embedding models and support functions.
... |
a828b75f40262bc6f9e74e10e986b3dcd1be8aba71a3d0f2b432145abef15bfe | Python | 2,330 | 59 | """
Test construction of a complete circuit build from cell populations.
This script:
1. Creates populations of sgc, bushy, and stellate cells.
2. Connects the populations together.
3. Instantiates 10 bushy and 10 t-stellate cells near 16kHz.
4. Resolves all required synaptic dependencies.
No simulation is executed;... |
de2ce3dd8372c9d92328ad62cd1e44312add28df6d64f09015ca88aa36464406 | Python | 2,330 | 48 | # Copyright 2019-2020 The ASReview 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 appl... |
c97ad718379f5e2a407640793c4a5d793bdc7a98e3565518483f52013b2c9bd8 | Python | 2,332 | 78 | import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib import cm
from matplotlib.colors import ListedColormap, LinearSegmentedColormap
import seaborn as sns
mpl.rcParams['pdf.fonttype'] = 42
mpl.rcParams['ps.fonttype'] = 42
mpl.rcParams['font.family'] = 'Arial... |
5e42b926b9a3770ad069b1d543d17f07dc158d93ca11fa5cd89ccaa5c34a7445 | Python | 2,335 | 71 | # 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... |
9984918778b47a2fddb5266ca20c7055a575c4ddd6b7cd009fc7b71ac84f6937 | Python | 2,335 | 62 | import argparse
import csv
import pickle
from tqdm import tqdm
import time
from rxnebm.data.preprocess import canonicalize
parser = argparse.ArgumentParser()
parser.add_argument('--output_format',
type=str,
default='gln',
help='["gln", "retroxpert"]')
# TODO... |
9e9d197590b54ff43f11f2116f3d1f29b9517894401efaa5729ce5e809f81bdc | Python | 2,336 | 75 | # -*- coding: utf-8 -*-
#
# Copyright © 2013 Charles E. Vejnar
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
"""Interface with the `Cufflinks <http://cole-trapne... |
defa20ee9f4652123c0a3ee851652a0f6ca962fa64f2b9bc43e2295a8f59276e | Python | 2,336 | 73 | # Copyright 2019-2020 The ASReview 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 appl... |
ab55aad5ae9b5858dacf21813aed972443d3ad7902f9bdda8733a41291b8bcac | Python | 2,337 | 72 | #
# # Visualizing a single network
#
# [Open interactive notebook in Binder](https://mybinder.org/v2/gh/wiheto/netplotbrain/main?filepath=docs/gallery/plot_connectivitymatrix.ipynb)
#
# ## Goal
# Here we are plot the nodes on the brain from the Schaefer atlas and plot the connectivity matrix next to it
#
# So this code... |
6ef88fb3dc5903c8af9981f49f72b093b6167a115dcea2f91a331364604380ef | Python | 2,339 | 59 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import os.path as osp
import numpy as np
from mmcls.datasets.pipelines import LoadImageFromFile
class TestLoading(object):
@classmethod
def setup_class(cls):
cls.data_prefix = osp.join(osp.dirname(__file__), '../../data')
def test_loa... |
3b48cdcf194f9fe34ff03d8412ed2be0120403756522eb53195e8f1d429d9269 | Python | 2,340 | 65 | import unittest
from pyontutils import combinators as cmb
from pyontutils.core import OntGraph
from pyontutils.namespaces import owl, rdf, rdfs, ilxtr
class TestCmb(unittest.TestCase):
def _doit(self, gen):
OntGraph().populate_from_triples(gen).debug()
def _doit_fail(self, gen):
try:
... |
acb98599cd165df91662134f8703b4d9fea00501b99123abe18ab5cbc00de163 | Python | 2,341 | 93 | from neuron import h
import numpy as np
import scipy
import scipy.integrate
import scipy.stats
try:
import pyqtgraph as pg
HAVE_PG = True
except ImportError:
HAVE_PG = False
from ..util.stim import make_pulse
from .protocol import Protocol
class CurrentClamp(Protocol):
def __init__(self):
sup... |
f136c82ced12b4dac91835d87bd20824524940d022a3b0d67e0d2027641efcd1 | Python | 2,345 | 61 | # 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... |
938bfae680bcd207ea03793990cca46a5bbc240b346df8e1f29a5101f45adb63 | Python | 2,347 | 76 | """Distribution plot of predicted per-read alignment penalties."""
import logging
from typing import Optional, Sequence
import matplotlib
# Select a non-interactive backend before pyplot is imported so the command
# works over SSH and in CI, where no display is available.
matplotlib.use('Agg')
import matplotlib.pyp... |
9d74380327bbadd73bbd92db40d8b5cbc973236a839cfc5aa4ce25f6af95a04c | Python | 2,348 | 76 | from __future__ import division
import os
import sys
import pandas as pd
from SPHARM.classes.surface import Surface
from helper_lib import filelib
from mayavi import mlab
#################################
args = sys.argv[1:]
if len(args) > 0:
path = args[0]
if path != 'test':
if not path.endswith('/'... |
5b47ff56917e4313b63a066dbd87c2a59852e8f0e7d6547cddaea9d27043e346 | Python | 2,349 | 107 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from onnx.reference.ops.op_pool_common import CommonPool
class AveragePool_1(CommonPool):
def _run(
self,
x,
auto_pad=None,
ceil_mode=None,
kernel_shape=None... |
76ea5ec4167c288d9ccab08214a6bdfb6a13249cd943df017660665aa42a4fcc | Python | 2,349 | 64 | from dill import load, dump
from mprl.utils import ensure_dir
class WeightsUtilsPolicyMixin(object):
def get_model_weights(self, remove_scope_prefix:str = None):
if remove_scope_prefix and not remove_scope_prefix.endswith("/"):
remove_scope_prefix += "/"
weights_dict = {}
f... |
7921fb28c1dac020030896b11d6adf3d6720ea4e6f27cc0278bf03c7f3018d34 | Python | 2,350 | 63 | """
This script will combine multiple LMDBs in a directory into a single LMDB dataset.
"""
import click
import sys
import pandas as pd
import lmdb
import io
import gzip
import logging
import tqdm
from atom3d.datasets.datasets import LMDBDataset, make_lmdb_dataset, serialize
logger = logging.getLogger(__name__)
@click... |
98c1ca83dbb1ab5757f3e346c11f409ce842ada929d302ede7929a5d7e3636c1 | Python | 2,350 | 66 | import pandas as pd
import pytest
from sktime.detection.bs import BinarySegmentation
from sktime.tests.test_switch import run_test_for_class
__author__ = ["Alex-JG3"]
@pytest.mark.skipif(
not run_test_for_class(BinarySegmentation),
reason="run test only if softdeps are present and incrementally (if requeste... |
952f4d234cd8d868ba60e5ea0e1a9028f5a2b7da096e4c7ac19290b977b89927 | Python | 2,351 | 85 | #!/usr/bin/env python
import click
from Bio import motifs
import logomaker
from matplotlib import font_manager as fm
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import warnings
warnings.filterwarnings("ignore")
# Specify font
f = os.path.join(os.path.dirname(os.path.realpath(__fil... |
638d63b1228589ddc155fd3048e93b8fe3f9ac9af061dcf7b4277ad49a291637 | Python | 2,353 | 67 | """
Parameters:
---------
subjects directory, subject name, hemi (should be defined in the main script curveball.py)
reads {h}.pial.ply and {h}.white.ply (outputs from mesh_pial_white.py scrips) files to
calculate the cortical thickness for each hemisphere.
Returns:
--------
{h}.thickness.asc for each hemisphere
""... |
87178b0a439f4e26beb8678f7836afe56cd0219dbd7c65ecb038a3f2e9b69747 | Python | 2,353 | 82 | """Longley dataset for forecasting with exogenous variables."""
from sktime.datasets._single_problem_loaders import load_longley
from sktime.datasets.forecasting._base import _ForecastingDatasetFromLoader
__all__ = ["Longley"]
class Longley(_ForecastingDatasetFromLoader):
"""Load the Longley dataset for forecas... |
d30ef2a5056e02b584fa761247a59ec70e584ccbee2e2569d98edea8e7b3a661 | Python | 2,354 | 58 | '''
Canonicalize product SMILES by re-assigning atom mapping numbers according to the canonical atom order.
Since the original mapping numbers may indicate the reaction atoms, which results in information leak.
'''
import pandas as pd
from rdkit import Chem
from tqdm import tqdm
from pathlib import Path
input_folder... |
75edb65c1fba5a8dd7aa8e8e82437480d6029c3ee88a1066d8916ef0010c1f3d | Python | 2,356 | 59 | #-------------------------------------------------------------------------------
# elftools tests
#
# Andreas Ziegler (andreas.ziegler@fau.de)
# This code is in the public domain
#-------------------------------------------------------------------------------
# The lib_relro.so.elf file was generated as follows (on Deb... |
5060163a032476af6fde467fc3fec4e56e2d0689eb8b16d8f9763130a26fe907 | Python | 2,359 | 47 | # Copyright 2019-2026 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 ampligraph.latent_features.layers.scoring import TransE
import pytest
im... |
626116cef91ebbdaf76633a5d62d75bceb63fc6a20889dc53d79d833078bcc57 | Python | 2,359 | 68 | from __future__ import annotations
from typing import Dict, List, Sequence
import numpy as np
Array = np.ndarray
def evaluate_usage_metrics(
pred_usage: Array,
y_usage: Array,
y_counts: Array,
groups: Sequence[Array],
eps: float = 1e-8,
) -> Dict[str, float]:
"""Evaluate predicted within-ge... |
f00b7d22b3883d7bfdb085f6ab9f6b6e9bb3acf2902b906dec518c06aaa08628 | Python | 2,359 | 69 | import re
from setuptools import setup
def find_version(filename):
_version_re = re.compile(r"__version__ = '(.*)'")
for line in open(filename):
version_match = _version_re.match(line)
if version_match:
return version_match.group(1)
__version__ = find_version('ttlser/__init__.py'... |
39d4527bcce91089301b56c351a9268519dd78291cbed6ca7e9060d2d931ddb3 | Python | 2,361 | 73 | # -*- coding: utf-8 -*-
import os
import numpy as np
import nibabel as nib
def float_in_filename(num):
""" Function to remove the "." of the float to avoid it in filenames.
It convert the Numeric input into a str
If the input is simply an int, it just converts it into str
Parameters
----------
... |
f5928afbf4c33a729447e551364ba3f5fad28c42dce3e2a7b3d887308ee8eb9c | Python | 2,361 | 54 | import torch
import flair
from flair.datasets import IMDB
from flair.distributed_utils import launch_distributed
from flair.embeddings import TransformerDocumentEmbeddings
from flair.models import TextClassifier
from flair.trainers import ModelTrainer
def main(multi_gpu):
# Note: Multi-GPU can affect corpus load... |
3a5f512bf6781ec71bd9362adc98b5be1cb38ab51a869df27efe453201ce7b82 | Python | 2,363 | 70 | """
This script is both a demo for those who are new to running LFADS
and a test script to rapidly test changes. The main steps to
running LFADS are:
1. Create a configuration YAML file to overwrite any or
all of the defaults
2. Create an LFADS object by passing the path to the
configuration... |
76210fbbb3cb74c5a2c1585adf2ea4762b32d0526d069e6cc97a0b56c65f3b2a | Python | 2,363 | 56 | import sys
import numpy as np
from parameterSetup import ParameterSetup
from evaluationCriteria import y2sensitivity, y2confusionMat, printConfusionMat, mathewsCorrelationCoefficient, multiClassMCC
args = sys.argv
test_path = args[1]
pred_path = args[2]
params = ParameterSetup()
stageLabels = params.stageLabels4evalu... |
f1ffd29042def789eecdadb94ada194f39f0194903ae432ed1571c4aa2f03c50 | Python | 2,363 | 81 | import numpy as np
from scipy.signal import periodogram
from numba import njit
@njit
def fill_feat_mat(
feat_mat: np.ndarray,
win_id: int,
Pxx: np.ndarray,
n_chan: int,
freq_idx: np.ndarray,
):
for ch in range(n_chan):
for kk, freq_lims in enumerate(freq_idx):
feat_mat[win... |
586139a0b5ae1e2ece9c468596890afde2aa81a0e487442b1738496aa2f7d57f | Python | 2,364 | 77 | # Copyright 2019-2021 The ASReview 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 appl... |
4e16e76971a34962a29616c66b75dbf06f8f8a9bc10c617812f70401d75064b2 | Python | 2,365 | 86 |
"""
Build synconfig (print to terminal) based on reading the ASA file
e.g., make this::
VCN_c18 = [ [(216.66), 0., 2, np.nan, np.nan, 49.2, 1.222, 'e' ],
[(122.16), 0., 2, 82.7, 1.417, np.nan, np.nan, 'e'],
[(46.865), 0., 2, 67.3 , 1.309, 62.1, 0.717, 'e' ],
[(84.045), 0., 2,... |
bd6af03fe14f56c6e1c1fe7ccea8fdba82af43ba1061b59da17cc27a496cfd61 | Python | 2,367 | 97 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 1 16:54:07 2022
@author: sudhanshu
Trains the CAPSIF:G model on the dataset
Note, must be run after preprocess.py has been performed
Usage: python train.py
Returns: prediction model into "models_DL/capsif_g_model.pth.tar"
"""
import egnn.egnn as... |
36358e3370b0ec6a59c07f11d4a27e063c0a0a87d6e0e7a56a1ea2ba14a33a09 | Python | 2,369 | 93 | # 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 Identity(Base):
@staticmethod
def export() -> None:
no... |
81dce7bbd2a010331ce9334e715dd956a9a4477b950966c2a9c3812b5f84552b | Python | 2,370 | 65 | # Short script used to create the blosum matrices necessary when using "use_blosum" argument
import pickle
import numpy as np
from sklearn.decomposition import PCA as PCA
alphabet='ARNDCEQGHILKMFPSTWYVX'
def subsmatFromAA2(identifier, data_file='aaindex2.txt'):
"""Retrieve a substitution matrix from AAindex2-file... |
aa8ec1816c40c1ccd606640ed9723b71168749ceb96be70e24fa90e9e7acf6a6 | Python | 2,371 | 68 | import pandas as pd
import numpy as np
from bids import BIDSLayout
import itertools
import os
def generate_group_cm(nodes, subjects, community_size, community_str, scale=0.25, seed=2022):
"""
Quick way to simulate group differences for visualization purposes.
Input
-----
nodes : int
numbe... |
4a5133a57c0143298c8800979b3905bf475ae1c1e95d6082b5d60a0518ff0ade | Python | 2,372 | 78 | """Tests for time series Lloyds partitioning."""
from collections.abc import Callable
import numpy as np
import pytest
from sklearn.model_selection import train_test_split
from sklearn.utils import check_random_state
from sktime.clustering.partitioning._lloyds import (
BaseTimeSeriesLloyds,
_forgy_center_ini... |
ff0d10338162a825b844d5b5b64b40ecc8a33c31ceee03cef68bf492ad28b82e | Python | 2,372 | 61 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.helper import tensor_dtype_to_np_dtype
from onnx.reference.op_run import OpRun
class MelWeightMatrix(OpRun):
def _run(
self,
num_mel_bins,
dft_... |
3dd35bdf597730ea808629cf3cb0be1b6c7bb710287a5e9638e8a9d4a505b443 | Python | 2,373 | 74 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""State-aware clone and set_params for arbitrary objects."""
__author__ = ["SimonBlanke"]
from sktime.base._base import _safe_clone
_VALID_TARGET_STATES = ("new", "pretrained")
def _check_target_state(state):
"""Raise ValueError if state ... |
3471d2ecbff51b951d79fb5bd6d7a281546508d71987574c27426d8eeda4e028 | Python | 2,378 | 91 | # 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 Gather(Base):
@staticmethod
def export_gather_0() -> None:
... |
fad004dc915d895092525dad91c725f0148a6667ca95c1fb99842b760391cf70 | Python | 2,378 | 77 | import torch
def pairwise_distance_sq(
p,
q,
norm_choice="cartesian",
device=torch.device("cuda" if torch.cuda.is_available() else "cpu"),
):
"""
Compute the squared pairwise distance between jet 4-momenta p and q.
Args
----
p, q: `torch.Tensor`
The 3- or 4-momenta of shap... |
fdb4d641a62e9f6c3e0dda513084c47b7e44783271c137efed8aa581780f77b1 | Python | 2,379 | 76 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Base classes for classification datasets."""
__author__ = ["felipeangelimvieira"]
from sktime.datasets.base import BaseDataset, _DatasetFromLoaderMixin
__all__ = [
"BaseClassificationDataset",
"_ClassificationDatasetFromLoader",
]
... |
676d625ba9d10393917edea2eeedaa247dc1d63e71b12043917097e090e3ee35 | Python | 2,382 | 88 | import numpy as np
from ..lddmm._lddmm_utilities import _validate_ndarray
def _verify_data_is_ndarray(data):
if not isinstance(data, np.ndarray):
raise TypeError(f"data must be of type np.ndarray.\ntype(data): {type(data)}.")
def cast_to_typed_array(data, dtype=float):
"""
Returns a copy of data... |
a1368de75646071f34d52880779e3c7eef9dc77cad8bb1a86838f5ad3921e40e | Python | 2,383 | 66 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 13 08:48:12 2021
@author: sam
"""
import os
import argparse
import configparser as ConfigParser
import glob
import shutil
from ssh_tools import retry_ssh
#%%
if __name__ == '__main__':
# Arguments used in run_pipeline
p = argparse.Argumen... |
8a8052ecf8d40990cfc86f6b4b50aa5689c9f77a9f4b03dbfde9f885a7415842 | Python | 2,384 | 71 | # 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... |
4e2e8949585dfb6d9eb969a60f4cdbe50b55a50abef32a0ce3a1c15316474031 | Python | 2,385 | 56 | # ----------------------------------------------------------------------------
# Copyright (c) 2017-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
1fc6977c9f65e244f34371cddc93096a8b72e848ad87fee0d842ea3ce22c1fe6 | Python | 2,386 | 75 | """Tests for igts module."""
import numpy as np
import pytest
from sktime.detection.igts import IGTS, InformationGainSegmentation, entropy
from sktime.tests.test_switch import run_test_for_class
@pytest.fixture
def multivariate_mean_shift():
"""Generate simple mean shift time series."""
x = np.concatenate(t... |
4e9df66b087e78e878220ee477f376dbdaec34e81a5f68931fe47455084a3f2f | Python | 2,386 | 68 | # 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 Less(Base):
@staticmethod
def export() -> None:
node =... |
b5caadbc5fe2854b9e70c8a6b4c04f9d724d1f51e069f0b87ca85f4c3021559c | Python | 2,386 | 78 | import numbers
import wandb
from ray import tune
from ray.tune.util import flatten_dict
import ray
def make_dict_items_yaml_representable(repr_dict):
for k, v in repr_dict.items():
if type(v) is dict:
make_dict_items_yaml_representable(v)
if isinstance(v, tuple):
repr_dict... |
45b9f644a7e6518e7f38b2780cf3892013192fb85fbdacc1e2499d5bb017f915 | Python | 2,390 | 59 | #!/usr/bin/env python
#
# Copyright 2019 Google LLC. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list o... |
6c6d700c147bf16eaffa4dd7c78348083d3fc7e8aeec0d5a01e0a3a91af0ace0 | Python | 2,393 | 64 | from typing import Union
import time
import pytest
import siibra
from siibra.core.structure import BrainStructure
from siibra.core.space import Space
from siibra.features.image.image import Image
all_image_features = [f for ft in siibra.features.Feature._SUBCLASSES[siibra.features.image.image.Image] for f in ft._get_... |
26ae352a8f47dbf19b0783bc8e70ce002f93910121a09e9bd3ad2d196718270d | Python | 2,394 | 84 | #!/usr/bin/env python
import click
from functools import partial
from multiprocessing import Pool
import os
import re
import subprocess as sp
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
os.pardir,
os.pardir))
... |
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