sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
439848d5189c697880fee45cf9dff5bb0f59334c7fd245652dfb865400937d37 | Python | 3,785 | 123 | """Tests for SubLOF"""
__author__ = ["Alex-JG3"]
import datetime
import pandas as pd
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.detection.lof import SubLOF
from sktime.tests.test_switch import run_test_for_class
def _daily_datetime_case():
"""Return daily Datetime... |
54a5dd364e3b4bb5d3754d3d23ac8c3315492d0b67d0bd71af100a3991751b56 | Python | 3,787 | 115 | from open_spiel.python.egt import alpharank
from open_spiel.python.egt import alpharank_visualizer
from open_spiel.python.egt import utils, heuristic_payoff_table
from open_spiel.python.algorithms.projected_replicator_dynamics import projected_replicator_dynamics
import numpy as np
def get_alpha_rank_pi(payoff_tabl... |
1e2e876bccc307538ac3174cf9464f73f4672ddecb7f413afc16b7148372417c | Python | 3,790 | 112 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""
Attention utilities for SeZM message passing.
This module implements the destination-wise envelope-gated softmax used by the
SO(2) attention path in the SeZM descriptor.
"""
from __future__ import (
annotations,
)
import torch
import torch.nn.functional as F
@to... |
2301aa0dbb22b1bbf831d9a15e7bbdc27eea495c135cebfac28bc3e7341a829b | Python | 3,790 | 79 | #=======================================================================================================================
# Copyright (C) 2021 Matvey Safroshkin, Grigory Arutyunov, Patrick Mueller
# Computer Vision Studio
# Friedrich Miescher Laboratory of the Max Planck Society
# Systems Biology of Development, Univers... |
2bda2b5dad17b1b0bddc67aaaa61e3d5fa90a0d138da44a6eadb63590a730c68 | Python | 3,790 | 106 | """Unit tests for all time series regressors."""
__author__ = ["mloning", "TonyBagnall", "fkiraly"]
import numpy as np
import pandas as pd
from sktime.datatypes import check_is_mtype
from sktime.tests.test_all_estimators import BaseFixtureGenerator, QuickTester
# Pairs of message and lambda function to check the t... |
bab2be6fc796da54997dcdd3bc9033eff34dfbefc1cba798156d560481feee26 | Python | 3,790 | 122 | import re
import os
import sys
from pathlib import Path
from setuptools import setup
def abspath(relpath, _dir=os.path.dirname(__file__)):
return os.path.join(_dir, relpath)
def find_version(filename):
abs_filename = abspath(filename)
_version_re = re.compile(r"__version__ = ['\"](.*)['\"]")
last = ... |
3b5c09f12942dd515ef194c51465f778b4451845bb25699da95a4281bb52a1ec | Python | 3,792 | 116 | import pytest
import numpy as np
import pandas as pd
import scanpy as sc
from anndata import AnnData
from scipy.sparse import csr_matrix
from anndata import AnnData
from palantir.utils import run_magic_imputation
@pytest.fixture
def mock_dm_res():
rng = np.random.default_rng()
return {"T": csr_matrix(rng.ran... |
4b70398daf64a3edc4fc944c247e307bdf09713ba5f25f8cc175db8c52cff16d | Python | 3,793 | 112 | # 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... |
e082703e3770de45fd5a1f26e9b38df1a7e1cc3eac32c31219e3702d6728c267 | Python | 3,794 | 60 | rgb_colors = {'Xx': (0.07, 0.5, 0.7), 'H': (0.75, 0.75, 0.75),
'He': (0.85, 1.0, 1.0), 'Li': (0.8, 0.5, 1.0),
'Be': (0.76, 1.0, 0.0), 'B': (1.0, 0.71, 0.71),
'C': (0.4, 0.4, 0.4), 'N': (0.05, 0.05, 1.0),
'O': (1.0, 0.05, 0.05), 'F': (0.5, 0.7, 1.0),
... |
c9a17e214369e82a9102af26c989277b9cf3710c5ea154d72509b8b6932fcd31 | Python | 3,796 | 157 | # 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... |
1c089b52a77146a1dce912167be79a5233c4210dfa3ff03116a718cfedaa22bc | Python | 3,799 | 73 | import warnings
import torch
from vp_suite.measure import METRIC_CLASSES
class PredictionMetricProvider:
r"""
This class provides bundled access to multiple metrics. With this class's :meth:`get_metrics()` method,
all specified metric scores are calculated on the same input prediction and target... |
2d1b964630ead10200e9726e1f291209eb27ad3820c05c82bb37cc5a45acd44a | Python | 3,800 | 126 | # Copyright 2018-2026
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
c802b47716be27441d587478f804f1eab26729dcf93c533e73baf797bf13d490 | Python | 3,800 | 80 | import tensorflow as tf
from tensorflow.contrib import distributions as distr
class SingleLayerDecoder(object):
def __init__(self, config, is_train):
self.batch_size = config.batch_size # batch size
self.max_length = config.max_length # input sequence length (number of cities)
self.... |
60915dd953bf8703d2cccd8d71b5a9e14ebacb680f5f243d26da2bcda623d62f | Python | 3,804 | 104 | """
@file: wide_resnet_se.py
Created on 07.04.19
@project: CrazyAra
@author: queensgambit
Please describe what the content of this file is about
"""
from mxnet.gluon import HybridBlock
from mxnet.gluon.nn import HybridSequential
from DeepCrazyhouse.src.domain.neural_net.architectures.a0_resnet import (
_ValueHead... |
ae8062a7a6f45a8725f099a8eaae5352182a450760f2faab4ba6f0b306ec4d44 | Python | 3,804 | 88 | """
Regional surface data generated from the Brodmann atlas. The label files are generated using Freesurfer.
From label files, the vertices the belong to each spcific region are extracted. And from that information
the surface files for each region are saved.
Parameters:
---------
{h}.{l}.label: Label files of ea... |
bf998dba41c1bd14dd5cab127fdd60c8cbff9c76c23406ab69ed09b397b06e18 | Python | 3,804 | 128 | # type: ignore
# 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 -------------------------------------------------------... |
91359cf5f3b5c989423899bbc42dd88bb499a7787b17efe8bbce4fbba6ff04f5 | Python | 3,806 | 136 | """Tests for bcblib.imaging.stats."""
import numpy as np
import nibabel as nib
import pytest
from bcblib.imaging.stats import (
centre_of_gravity,
centre_of_gravity_distance,
volume_count,
laterality_ratio,
reduce_axis,
image_stats,
percentile,
robust_range,
histogram,
)
def _mak... |
66ec404198c5f46219433565e3a84debd23e78f6c85eaaf037fcc5d6d49fe29e | Python | 3,807 | 114 | from __future__ import annotations
from pathlib import Path
import numpy as np
import pytest
from jetnet.datasets import TopTagging, normalisations
from pytest import approx
# TODO: use checksum for downloaded files
data_dir = Path("./datasets/toptagging")
DataClass = TopTagging
valid_length = 403000
num_particle... |
3c823b970cbdd96675c53872c18bcc964138adf5c103469e24f8fb9987cfcc78 | Python | 3,810 | 79 | import logging
# PyTorch modules
import torch
from torch.utils.data import DataLoader
# Cormorant modules and functions
from cormorant.data.utils import initialize_datasets
from cormorant.engine import Engine
from cormorant.engine import init_logger, init_cuda
from cormorant.engine import init_optimizer, init_scheduler... |
443d21831ef3a5a2b155f0a28e47df70619fe7dd4e0d9af9159f1905f5aa67b5 | Python | 3,811 | 112 | # Copyright 2018-2026
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
74b0525c4ae5998d6dec340f1a1f8f5c270d552ac205e50beeaf4a4546f17daf | Python | 3,814 | 115 | # 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... |
7fbbf0543bdc8b35e4ed531eac98ea1698e676e3358bd60a106babfe9fa8dead | Python | 3,816 | 105 | # 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... |
c486c638b01345b24860d25ff65fc05fcd6c7d13868e76d46e1f7e241de7fa4f | Python | 3,816 | 107 | # 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... |
ac0239f5ee03fe3ebb00797af58a39b7db31299af4e704bea9f8eb1d6594bf9a | Python | 3,821 | 104 | import pytest
from typing import Union, List
from json import JSONDecodeError
from requests import RequestException
from functools import wraps
import siibra
def xfail_if_allen_api_unavailable(test_func):
@wraps(test_func)
def wrapper(*args, **kwargs):
try:
return test_func(*args, **kwargs... |
48b21b6f1e1212cb1821f2ac52d5222d6b25255b9f7b5b358f51d3a1d716c1e9 | Python | 3,823 | 122 | import numpy as np
from scipy import stats
# AUC comparison adapted from
# https://github.com/Netflix/vmaf/
def compute_midrank(x):
"""Computes midranks.
Args:
x - a 1D numpy array
Returns:
array of midranks
"""
J = np.argsort(x)
Z = x[J]
N = len(x)
T = np.zeros(N, dtyp... |
84a30e695d539ca2aa15a49965fa71f6dbd09ebbf2dc177951915cb46f6bbbcf | Python | 3,823 | 111 | # 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... |
6313d8a5300e7b89b73a222bbfa2f2668c296e7d83dbc020e3199a0a81b5d38f | Python | 3,825 | 124 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
# mypy: ignore-errors
from __future__ import annotations
import numpy as np
import onnx
import onnx.helper as oh
import onnx.numpy_helper as onh
import onnx.reference as orf
def create_model():
"""The following model is equivalent ... |
8b1ddaa75f9c09f18495e864fb0504b0cc52b16de77bab8504ce0cec48ab3569 | Python | 3,827 | 121 | # Copyright (c) OpenMMLab. All rights reserved.
import functools
import torch
import torch.nn.functional as F
def reduce_loss(loss, reduction):
"""Reduce loss as specified.
Args:
loss (Tensor): Elementwise loss tensor.
reduction (str): Options are "none", "mean" and "sum".
Return:
... |
2905a5a02591448f482b0903a06a1f289827555543d45b2555c4e7a8887c982f | Python | 3,829 | 75 | """
Utility functions for dealing with network colors.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IMPORTS
"""
import warnings
SETOFVALIDCOLORS = {'aliceblue', 'antiquewhite', 'aqua', 'aquamarine', 'azure', 'beige', 'bisque', 'black'... |
ba594d3fd9b99d4ee2610b4e2dec6405a06ed9583073e209bdfa98f098dcae8a | Python | 3,831 | 112 | # 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... |
c0dff3d2e6d2a66fe41611ae422b6580d5d2921c50df778dd5c61dcb29bef33b | Python | 3,832 | 120 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Test script to check for invalid use of single-backticks."""
__author__ = ["geetu040"]
import argparse
import ast
import glob
import re
def find_py_files(folder_path):
"""Find all Python files in a given folder... |
01222036d36f35be629d9eac7c2a34c156c96fd73757ea3f8e2bf90c739033db | Python | 3,836 | 138 | from typing import Tuple
import torch
######### Weight mixing ###########
def mix_zweight_zvec(weight, part, zdim=0):
"""
Apply the linear matrix in `GWeight` and a part of a `GVec`.
Parameters
----------
weight : `torch.Tensor`
A tensor of mixing weights to apply to `part`.
part :... |
3aec8ae42843feda8d4695ae822649d0e7ae499a95fb41411f5128ada65e221c | Python | 3,836 | 113 | # 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
#
import os
import importlib
import numpy as np
import pandas as pd
import numpy.... |
ad7d239c3ad5bb22856713459db8a27982c46b1394c91bb83973739bbc4cd954 | Python | 3,837 | 60 | import numpy as np
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
import seaborn as sns
sns.set(font_scale = 1.5)
sns.set_style("ticks")
# fitting function
def eq_5_fitting_mM(V,conc,alpha, eta):
return 1/(1+conc*eta*np.exp(alpha*V))
simulated_voltage=np.linspace(-250,150, 1000)
simulated_... |
cc70c27dc46ab93d756161c51e636133bba5260e7d9152009be00e753895306a | Python | 3,838 | 102 | # 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... |
d55acfa525738923104a2b29ad98aaa3ea281a39fea3047eef198088048dc251 | Python | 3,840 | 102 | import sys
import pickle
import numpy as np
from parameterSetup import ParameterSetup
#--------------
# print in the format of a latex table
params = ParameterSetup()
pickledDir = params.pickledDir
paramDir = params.pickledDir
args = sys.argv
if args[1] == 'test':
datasetType = 'test'
groupIDs = args[2:]
eli... |
cc6e8ad0157633881a0ced4369f5244b6d2ad704347b104e9bdc984ae0e3fb81 | Python | 3,841 | 102 | """
@file: input_representation.py
Created on 03.07.23
@project: CrazyAra
@author: queensgambit
Input representation 3.0 for crazyhouse based on the input representation 3.0 of chess.
"""
import chess
from chess.variant import CrazyhouseBoard
import DeepCrazyhouse.src.domain.variants.classical_chess.v3.input_represent... |
5734e715dd3817898f36dd4858effd3d4943dc286bcc27012e3a87475e020900 | Python | 3,842 | 98 | from __future__ import print_function
import dxpy
import subprocess
import time
app_id_hardcode_up_version={
"app-FPkkQ4j0gjx97J1X1496B9zF":"purge_haplotig (bitbucket v1.0.3+ 1.Nov.2018)",
"applet-FZzYjYQ0j3b9pVP06qg4Q97Y": "purge_dups github ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b",
"applet-Fb721zj0j3b1... |
70e7c489327504b3b584ccef9a2a6398811d7d0a008b6c80112071ff22d94417 | Python | 3,843 | 108 | #!/usr/bin/env python3
import inspect
from pathlib import Path
from git.repo import Repo
from rdflib import Graph, URIRef
from neurondm import *
from pyontutils.utils import subclasses
from neurondm.core import NeuronBase, auth, ont_checkout_ok # FIXME temporary until we can rework the config
__all__ = [
'AND',
... |
32f61ec9de996bed3c4eda17bdb898056b3ad7c25800308c430db122d1817718 | Python | 3,844 | 113 | # 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... |
4c7e0f6958aea5a0c5dcf350e524f5fda1b217296393a99c2b1289e422f10d0c | Python | 3,845 | 157 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""NeighborGraph: backend-agnostic edge-graph neighbor-list subsystem.
The unified edge/graph neighbor-list contract and its supporting machinery:
``graph`` (the ``NeighborGraph``/``GraphLayout`` contract + derived node-validity
+ edge padding), ``csr`` (backend-agnostic CS... |
ba44635906f5f3f20312ce397e951e8a393caf663f22f892dc8842c3cd03d0ba | Python | 3,846 | 128 |
import matplotlib as mpl
from matplotlib.colors import to_rgba, to_rgba_array
from numpy.testing import assert_array_equal
from seaborn._core.plot import Plot
from seaborn._marks.area import Area, Band
class TestArea:
def test_single_defaults(self):
x, y = [1, 2, 3], [1, 2, 1]
p = Plot(x=x, y... |
d2c53e42f47bc2ec956c102019f5580d2feabcc3ff208796c9e0f3798c2920f3 | Python | 3,846 | 108 | import sys
import numpy as np
import nengo
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
sys.path.extend(['/home/will'])
from e... |
027a7be3d3fbfed7c9fccaee3779a2bc57312bc73ccc2e56b33833d91adf6c77 | Python | 3,847 | 112 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 26 10:10:25 2020
@author: sam
"""
from detectron2.data import MetadataCatalog, DatasetCatalog
from detectron2.utils.logger import setup_logger
setup_logger()
import os
import cv2
from detectron2.engine import DefaultPredictor, DefaultTrainer
from d... |
f8556f37b12d110125761ba1d8150d08f5e924273830504ecf15fd421f87b6d0 | Python | 3,847 | 167 | import torch
import numpy as np
""" FFT, iFFT, and FFTshift function """
def generic_fftshift(x,axis=[-2,-1],inverse=False):
"""
Fourier shift to center the low frequency components
Parameters
----------
x : torch Tensor
Input array
inverse : bool
whether the shift... |
d2940d3711a4d214cd3df337a080c4c4837386023fe13e5c13a4102178db4369 | Python | 3,848 | 94 | """encoder.py"""
"""
Ref: https://github.com/The-AI-Summer/self-attention-cv
Author: Yimin Yang
Last revision date: Jan 18, 2022
Function: Encoder of AA_TransUNet
"""
from einops import rearrange
from utils import *
class ViT(nn.Module):
def __init__(self, *,
img_dim,
in_channe... |
8e841c302165fa757d005e0e39915002f313ec30dc3bf19c255c16ba0a315e46 | Python | 3,852 | 117 | import numpy as np
import cv2
from data.utils import vx_vy2v_theta
def plot_evolution(gt, pred, mask, fps, filename = 'comparison.mp4', scale_frame = False):
n_frames = gt.shape[0]
H = gt.shape[2]; W = gt.shape[3]
## Ground-truth frame generation
gt_Lab = np.zeros((n_frames, H, W, 3))
gt_vsinco... |
f9859dfd87b53ca4a4b4383087d767e67b013c4862a0f94a1ec39096af6bcbc1 | Python | 3,852 | 125 | # 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... |
15d53f84d5e4476d0d964de0532bb6e6be07b5a17d3ab38991acdbd5badd55a2 | Python | 3,853 | 120 | import re
from collections import defaultdict
from pyontutils.sheets import Sheet
from pyontutils.namespaces import ilxtr, TEMP, rdfs, skos, owl
from neurondm.core import Config, NeuronEBM, Phenotype, EntailedPhenotype, log, OntId
class NeuronApinatSimple(NeuronEBM):
owlClass = ilxtr.NeuronApinatSimple
shortn... |
129426b76de9915a3d6bdee06d7e7f51ce67287b8f3f66f556e9a7a9211c21e2 | Python | 3,855 | 102 | import collections as col
import logging
import os
import re
import sys
import click
import numpy as np
import pandas as pd
import atom3d.datasets.datasets as da
import atom3d.splits.splits as spl
import atom3d.util.file as fi
import atom3d.util.formats as fo
logger = logging.getLogger(__name__)
def _filter(data... |
d93917e831f1969bcdabbffa5ad3ef1d4b3a10b34433604a67b2b61be4b9d963 | Python | 3,855 | 141 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# Note: To use the 'upload' functionality of this file, you must:
# $ pip install twine
import io
import os
import sys
from shutil import rmtree
from setuptools import find_packages, setup, Command
# Package meta-data.
NAME = 'scCODA'
DESCRIPTION = 'A Dirichlet-Multin... |
95180432adb20a5e0a60cfcdaa153c562527caa84348b2ab9058fd559a7adec3 | Python | 3,858 | 141 | # 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... |
e15eaff6db9ccbd1f9ce447a15c7b6b0069cc3a05effbc50fde8cfc0f1f434cb | Python | 3,858 | 105 | """Test suite for numba distances with parameters."""
from collections.abc import Callable
import numpy as np
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.dists_kernels._numba_distances import distance, distance_factory
from sktime.dists_kernels._numba_distances._distance ... |
0752426a3a7008cc3eae9d67e7faa373d8da19efbad1a9ab2f8dc147866ccc5e | Python | 3,859 | 151 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 23 23:26:09 2021
Plot example narrow vs wide place fields for fig 4
@author: robert.mok
"""
import os
import numpy as np
import torch
import matplotlib.pyplot as plt
from scipy.stats import binned_statistic_dd
import itertools as it
maindir = '/U... |
36fbf6ceef752b31536d67107d69d7a4b051c625b1184c554151ed8eca45e658 | Python | 3,860 | 115 | # 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... |
97d24274aaad66963e518b5bddf010873cba4c237537bf8855122b93709b4cb9 | Python | 3,860 | 115 | # 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... |
d0472b47887ea97e75a5db9bb03362e28e994cc7939e49d622bc7c10636ee7f4 | Python | 3,862 | 142 | import random
import torch
from spikingjelly.clock_driven import functional
from poolingNet_cat_1res_mvsec import NeuronPool_Separable_Pool3d
from tqdm import tqdm
from mvsec_dataset_v2.mvsec_dataset_outdoor import MVSECDataset
from eval.vector_loss_functions import *
import math
# Enable GPU
... |
e027116ec80bf2d0cec754fec9e3788169a419d5c4816728f85199ec71aaa7fe | Python | 3,862 | 118 | import os
import cv2
import numpy as np
import torch
import torch.utils.data
from PIL import Image
import torchvision.transforms as transforms
class Dataset(torch.utils.data.Dataset):
def __init__(self, img_ids, img_dir, labels, img_ext, transform=None):
self.img_ids = img_ids
self.img_dir = img_di... |
42d82b81e5802867769cca539c7325c6ebd04565a111ce53e51b550abbb6d27f | Python | 3,865 | 127 | #!/usr/bin/env python
# coding: utf-8
import argparse
import os
import numpy as np
import logging
import fbpca
import itertools
import argparse
import anndata
from robustlink import utils
from robustlink.scf import clst_utils
from robustlink.scf import basic_utils
def pipe_singlemod_clustering(
f_ann,
... |
e816e4f790981c618bf4820d814e213d4ecf2bb81166a386e985454ce18c924f | Python | 3,865 | 96 | import random
import numpy as np
import cv2
import lmdb
import torch
import torch.utils.data as data
import data.util as util
class WGTDataset(data.Dataset):
def __init__(self, opt):
super(WGTDataset, self).__init__()
self.opt = opt
self.data_type = self.opt['data_type'] #lmdb or img
... |
dead18eaf21f28924cdf570c1498f76b5fb532f100be1fda9c89d042f0c4c418 | Python | 3,866 | 112 | import numpy as np
import pandas as pd
from sklearn.cross_decomposition import CCA
from sklearn.utils import check_array
from sklearn.utils.validation import check_is_fitted, FLOAT_DTYPES
from sklearn.metrics import silhouette_samples
class CCA_extended(CCA):
def __init__(self,*args,**kwargs):
super().... |
ba0c309ab76d46204c305fe7861eb18246349d26328ad9ed061126ab24896ff8 | Python | 3,869 | 134 | import rdflib
import augpathlib as aug
from pyontutils import sheets
from pyontutils.core import OntGraph, OntId, populateFromJsonLd
from pyontutils.config import auth
from pyontutils.namespaces import (rdf, rdfs, owl, ilxtr, NIFRID,
definition, editorNote, OntCuries)
from pyld.jsonld... |
e564e6f35599676a348a65248324a8414ff8e7dc88bd251c82de0048940734b5 | Python | 3,870 | 99 | # Copyright 2017 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 applicab... |
106b972da9a1362cc05a5ed3d595b31d8db68b7090e41a9da1375a0f77e9465d | Python | 3,874 | 77 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
"""Create a PCA shape model from a set of pre-aligned contours.
Thi... |
6ee35cd0e8e5eebdb444c699326b0083328726c37aa02a0ca9c80655bb30f88b | Python | 3,874 | 98 | # 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... |
f7189c5a19e0eefb400af10ce191d8065bbec460a8fdf722aa2f70edde8095ac | Python | 3,874 | 106 | #!/usr/bin/python
#
# Author: Patrick Ohly <patrick.ohly@intel.com>
# Copyright: Copyright (C) 2015 Intel Corporation
#
# This file is licensed under the MIT license, see COPYING.MIT in
# this source distribution for the terms.
# Runs a command, pipes its output to stdout, and injects status
# reports at regu... |
9c136a2e8c78e96f1a0b6ccd50082e3791df433dd81d98e3744ddb4f606b0fde | Python | 3,875 | 111 | import copy
from flair.data import Sentence, Relation
from flair.tokenization import SegtokTokenizer, SpaceTokenizer
def _create_annotated_sentence() -> Sentence:
"""
Creates a complexly annotated sentence for testing.
"George Washington went to Washington."
- Sentence-level label
- "George Washin... |
b8e815960c231a0111dc0da783f4c4b2f7ae18b2a99fbdb79f7d8056480b9303 | Python | 3,876 | 75 | """
Functions which are used within the design subpackage, but may not be necessary for the end user.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IMPORTS
"""
import warnings
SETOFVALIDCOLORS = {'aliceblue', 'antiquewhite', 'aqua', '... |
d23a4ebe53c90ebd4c8515e4de4758da537ae9514a2b13d68f7eae74fd37884a | Python | 3,878 | 82 | import os
import torch
from torch.utils.data import Dataset
import numpy as np
from .indexes import *
class MVSECDataset(Dataset):
def __init__(self, root:str, split: int, condition: str, transform=None):
assert split in [1, 2, 3]
assert condition in ['train', 'valid', 'test']
... |
057532e7cd706c9973c62bd6aef91ae7b1ed3ed59663d3a62508dcf5b8054775 | Python | 3,879 | 127 | #!/usr/bin/env python
import click
from functools import partial
from multiprocessing import Pool
import os
import pandas as pd
from pybedtools import BedTool
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.p... |
eb041cc333b0fce740c3a01dc98f81d8dbd12d487c4ed5848097f5808a94943f | Python | 3,884 | 84 | """
hyperparameters for the pciSeq method
"""
import numpy as np
DEFAULT = {
# list of genes to be excluded during cell-typing, e.g ['Aldoc', 'Id2'] to exclude all spots from Aldoc and Id2
'exclude_genes': [],
# Maximum number of loops allowed for the Variational Bayes to run
'max_iter': 1000,
#... |
e9b7bbd94fa09a58a396368606f79ec3c81254b9b48c2cbb33dd404dec508598 | Python | 3,885 | 104 | # 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... |
63c932475c5b83115d3608fe32f468cf9e748016614930ae9544671937595aac | Python | 3,886 | 105 | # 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... |
0d8cdf51301ac4d23b4bc3b4e6ed784c6e891959eea396045eb537ba10b0c5e0 | Python | 3,887 | 131 | # 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... |
9c5985d0d57a8c680d9d9e25c66f9c2e4bbeadcb36398247509b827b349343ec | Python | 3,887 | 112 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
from ..builder import LOSSES
from .utils import weight_reduce_loss
def asymmetric_loss(pred,
target,
weight=None,
gamma_pos=1.0,
gamma_neg=4.0,
... |
fa863aa9aa6a817da26f191a0433bd4966b4fe6fe7df1f9d8f69940ce41f2750 | Python | 3,887 | 112 | # 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... |
bef802c5e082449a481263af6d57b1c012b2c4c6df56f2355031f9594aef4b63 | Python | 3,889 | 94 | """ entrainment.py - calculate spike entrainment for a periodic stimulus
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R01 DC015901 (Spirou, Manis, Ellisman),
DC R01 DC004551 (Manis, 2013-2019, Early development)
DC R01 DC019053 (Manis, 2020-2025, Later development)
Distributed under M... |
963b87b1caeb8ee8152301f6654cdca283ff0b5fb6dda90150063f86df1d97db | Python | 3,892 | 103 | from sklearn import metrics
import numpy as np
import torch
import importlib
import sys
import OT_crispr_attn
import torch.nn.functional as F
config_path = ".".join(["models", sys.argv[1]]) + "." if len(sys.argv) >= 2 else ""
config = importlib.import_module(config_path + "config")
class Ranking(object):
def __i... |
48bd74f896f4015b9accd6cda4f6bbae21d9a39ed904f8128554b492308837d7 | Python | 3,894 | 87 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
"""Plot a set of contours, optionally showing the ordering of their ... |
0edcd2bd310fdf6f7b5ab5ecb1eed1823dab0f0fb768f8a4516015323c46a1bf | Python | 3,896 | 95 | #!/usr/bin/python
import numpy as np
import pickle
import math
import gzip
import argparse
from itertools import islice
'''Convert Hi-C data from HiC-DC+ normalized (txt.gz) format to diagonal.txt
Usage Example:
[yangr2@lilac-ln02 script]$ screen
(base) bash-4.2$ bsub -n 2 -W 40:00 -R 'span[hosts=1] rusage[mem=64]' ... |
6dbddb019d142b62d3b5febd1f847a2480539f654053924fc8e15cdf6c467766 | Python | 3,896 | 144 | #%% [markdown]
# # Simulation
#%%
import datetime
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from graspologic.simulations import er_corr
from pkg.io import FIG_PATH, OUT_PATH
from pkg.io import glue as default_glue
from pkg.io import savefig
from pkg.match... |
a0b98b9d1d19b6a7f12eae46c0b47d1515240415f75fa935d75ca4bcdd16e122 | Python | 3,896 | 103 | from allennlp.predictors import SentenceTaggerPredictor
from akkadian.data import dump_object_to_file, load_object_from_file, compute_accuracy
from akkadian.build_data import preprocess
from akkadian.hmm import hmm_train, hmm_preprocess, hmm_viterbi
from akkadian.memm import memm_train, build_extra_decoding_arguments, ... |
6c447234582b3919599ee81d6fe38ee5a7fd243f70764eaf3e3c7cc238395f38 | Python | 3,899 | 105 | # 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... |
ce29df4c936877e4df49cbfe77ce7f3015083d71647abf804a738a78e7b027b2 | Python | 3,900 | 106 | # 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 pow(x: np.ndarray, y: np.ndarray) -> np.ndarray: # noqa: A001
retur... |
09d4abfcdcfda0a4e680b7b01ee40de377d5b778ec64026b394776116876f5d7 | Python | 3,903 | 124 | from jetnet.datasets import TopTagging, normalisations
import numpy as np
import pytest
from pytest import approx
from torch.utils.data import DataLoader
# TODO: use checksum for downloaded files
data_dir = "./datasets/toptagging"
DataClass = TopTagging
valid_length = 403000
num_particles = 200
split = "valid" ... |
1da545868dd8a857ed2d0dcd067755321d427239acbaf7c886af0861c9d1e620 | Python | 3,905 | 117 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
658470cd297f83dcfc35355ecbd4e2ca1f7fd3660b9ed31155e6593ee28fdb58 | Python | 3,905 | 118 | import numpy as np
from keras.optimizers import *
import os
import pandas as pd
from scripts import models_util
from scripts import training_util
import scipy as sp
import keras
# Global dictionaries
name_to_optimizer_dict = {'Nadam': Nadam, 'SGD': SGD, 'RMSprop': RMSprop, 'Adagrad': Adagrad, 'Adadelta': A... |
164f389e8b55edffe6fc22208dff443bcbf2db1bdd3561ce595f980e1df9167a | Python | 3,907 | 123 | import numpy as np
import cv2 as cv
import img_processing as img_utils
def predict_Q_values_of_section(img_path, sl_value, sgc_model, ql_model):
q1_value, q2_value, q3_value, q4_value, q5_value = 0, 0, 0, 0, 0
original_img = cv.imread(img_path)
if sl_value < 24:
# Send to registration
sect... |
463f39cb610c3d87924c87050c9aabe48129f6bd47767aa7bed8a6069ccf8796 | Python | 3,907 | 119 | #!/usr/bin/env python3
import rospy
import numpy as np
from std_msgs.msg import Float32MultiArray
from geometry_msgs.msg import Twist
from sensor_msgs.msg import LaserScan
from rospy.numpy_msg import numpy_msg
import torch
from sns_toolbox.networks import Network
from sns_toolbox.neurons import NonSpikingNeuron
from s... |
676d187896f09a64f02a13ab76e58d3d20d19af2a9b6407411f06a986ca99a77 | Python | 3,907 | 123 | # 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.helper import make_tensor
class TreeEnsemble(Base):
@staticmeth... |
73636f1faa0959cb423e5bcaa4a0fde20730a088cc239c1256ca251983accc0e | Python | 3,909 | 136 | import sys
from cyvcf2 import VCF
import numpy as np
from matplotlib import pyplot as plt
import seaborn as sns
from sklearn.metrics import roc_curve
np.random.seed(42)
colors = sns.color_palette()
dpi = 120
# python ab-truth.py eval/fp.vcf.gz eval/tp.vcf.gz eval/fn.vcf.gz
fp_path = sys.argv[1]
tp_path = sys.argv[2... |
2c107f7f55eb09d6f77d62c6c62cffdb3cf16ca39a9be60494e1ff51962cd871 | Python | 3,910 | 98 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Unit tests for (dunder) composition functionality attached to the base class."""
__author__ = ["fkiraly"]
__all__ = []
import pytest
from sklearn.preprocessing import StandardScaler
from sktime.classification.compose import ClassifierPipeline
... |
8fa23b14095106ad49936df6ce225b95b29756d0a4e24eeacbe6270b656c8e67 | Python | 3,910 | 103 | # 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... |
572902167f12c58bbad427a0e3e4df1db65ee95aafb8891d6240fc8e21154e12 | Python | 3,912 | 126 | # 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.reference.ops.op_rms_normalization import _rms_normalization
def c... |
df8a2556471f9a61a6c975d3967b6d113e077d90fadaa52746f05bd2173cb879 | Python | 3,912 | 108 | """
Author: Yifan Jiang (yifanyifan.jiang@mail.utoronto.ca) and Peidi Xu (peidi@di.ku.dk)
Description: Given a bifurcation, finds the optimal position of the branching point
and the optimal radii.
"""
import numpy as np
from scipy.optimize import minimize
class GD_Optimizer:
def __init__(self, loc... |
93c909f3edd833187cdc5c2c24b211b6afc47b4ad6d55095ba6ec1d2c550d6a8 | Python | 3,913 | 119 | from __future__ import annotations
from dataclasses import asdict
from dataclasses import dataclass
import json
import mimetypes
import os
from typing import TYPE_CHECKING
import uuid
from optuna._convert_positional_args import convert_positional_args
from optuna.study import Study
from optuna.trial import FrozenTria... |
f1b76980e23d39c341919887c06ae38d8b908a42419a7a58feafdf5600cfa3ec | Python | 3,913 | 162 | import _pickle as pickle
import sys
from scipy import stats
import numpy
import multiprocessing
print('''$1: Index Data\n$2: Output file''')
INDEX_DATA_FILE=sys.argv[1]
OUT_FILE=sys.argv[2]
class Person_PCC_Data:
import numpy
def __init__(self, EXP, POOL_LENGTH, PCC_POOL,header):
self.EXP = EXP
... |
2419a8f123113271502df8f27dcead88249c915f1a7e93d5f3d7bf6348d49850 | Python | 3,914 | 114 | import io
import os
import tarfile
import threading
import time
from concurrent.futures import ThreadPoolExecutor
import pytest
from siibra.retrieval import cache as cache_module
from siibra.retrieval import repositories
from siibra.retrieval.cache import CACHE
def make_tarball(path, files):
"""Write a tarball ... |
a5c715839c3687ad27165d38634e5fb5da55178c6da57e49c57275a281473c88 | Python | 3,914 | 136 |
import numpy as np
import pandas as pd
import pytest
from pandas.testing import assert_frame_equal
from seaborn._core.groupby import GroupBy
from seaborn._stats.aggregation import Agg, Est
class AggregationFixtures:
@pytest.fixture
def df(self, rng):
n = 30
return pd.DataFrame(dict(
... |
6db3af834b504b31862f9806071ad7f8a8112e1924f17c924641da4de25c327e | Python | 3,917 | 108 | # 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... |
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