sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a402556faf318df5ec0c18d4c9fb912f4d39fdc8490dbdf3164551a6f8ca45dd | Python | 972 | 35 | def win_ops():
data = ""
with open("D:\\Repos\\LungTumorSegmentation\\Resources\\train_data_win.yaml", "r") as f:
data = f.read()
data_split = data.split("label")
new_data = ""
ds = []
for i in data_split[3:]:
ds.append(i.split(",")[0].split("\\")[2].split("'")[0])
for... |
ed1bf14e2ba90e2b04da6d35469b213daa867b6d7ee90b031b4d3f638edbb32a | Python | 972 | 36 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.utilities.data_splitters.data_splitter module."""
from abc import ABC, abstractmethod
from typing import Iterable, List, TypeVar
T = TypeVar("T")
class DataSplitter(ABC):
"""Base class for data splitting.
This class s... |
3ecaa2b660776c4c5d5403125a3530475e520656f93c8893783d0a7385d42d51 | Python | 973 | 40 |
class Parameter:
def __init__(self, title, fieldType, default):
self.descriptor = {
"title" : title,
"fieldType" : fieldType,
"default" : default
}
class ParameterBase:
def getBuildTree(control):
"""Creates a build tree from the list... |
59e9f11312dab803a09153c43aaf18a37747e566637835eca2a221f56c89f1f3 | Python | 973 | 29 | from pymonntorch.NetworkCore.Behavior import Behavior
from sympy.physics.units import convert_to, second, seconds
class Clock(Behavior):
def __init__(self, *args, step="1*ms", **kwargs):
super().__init__(*args, step=step, **kwargs)
def initialize(self, neuron_or_network):
super().initialize(... |
db156591626380adf6346620e3ece9f88e78fb78d34d675b2cd63e55aafd3229 | Python | 975 | 29 | import numpy as np
from dival.evaluation import TaskTable
from dival.measure import PSNR, SSIM
from dival.reconstructors.odl_reconstructors import FBPReconstructor
from dival.datasets.standard import get_standard_dataset
np.random.seed(0)
# %% data
dataset = get_standard_dataset('ellipses', impl='astra_cpu')
test_dat... |
a54ebef755c2cc7a3434101c92200c8f63f2eb9e0792b6ea1f9722e2dba6e333 | Python | 976 | 32 | """Data classes for neuroimaging analysis.
`BrainData` (masked voxel data), `Adjacency` (similarity/distance matrices),
`DesignMatrix` (regressors), the `Roc` analysis class, the
`Simulator`/`SimulateGrid` data simulators, and the frozen result records those
classes return (`FitResult`, `PredictResult`, `BootstrapResu... |
aca10501560fa53f19e02934af8e436907cd083b544a83335d81f271e97fd847 | Python | 976 | 31 | import subprocess
import os
def extract_seqs(genomes_folder, output_folder, labels):
genome_files = []
for file in os.listdir(genomes_folder):
if file.endswith(".fasta"):
genome_files.append(file)
for genome_file in genome_files:
genome_name = os.path.splitext(genome_file)[0]... |
388114e3ae9ea784631880a21e041068bbd8aeef3192b7593a1406e7730cdd98 | Python | 977 | 31 | import unittest
from reinvent.chemistry import tokens
from reinvent.models.linkinvent.model_vocabulary.paired_model_vocabulary import (
PairedModelVocabulary,
)
from reinvent.models.linkinvent.model_vocabulary.vocabulary import (
create_vocabulary,
SMILESTokenizer,
)
from tests.test_data import WARHEAD_PA... |
dabc1de71c441cbbd7ea3039eb9a4905a7e561b88bff13209191685580168573 | Python | 979 | 37 | import os
import subprocess
import time
from collections import defaultdict, deque
import datetime
import pickle
from packaging import version
from typing import Optional, List
import torch
import torch.distributed as dist
from torch import Tensor
# needed due to empty tensor bug in pytorch and torchvision... |
dea206f9d8a9da248fcbecd641bb3290030de33aae74040bafeeb03a9046c9e5 | Python | 980 | 38 | '''
Remove words occur less than min_count times throughout the corpus
'''
import sys
import numpy as np
import pandas as pd
from scipy import sparse
import itertools
import os
w2cnt = {}
DATA_DIR = 'D:/UB/research/dataset/20newsgroups/'
def wordCount(pt):
print('counting...')
for l in open(pt)... |
0b672ea4ce2e7cd1e2f617ecdb5ba41d8bf6825d44cf6670e8c737f887139a1d | Python | 982 | 26 | from unittest import TestCase
from curtainutils.client import parse_curtain_from_json, CurtainClient
class Test(TestCase):
def test_parse_curtain_from_json(self):
json_path = r"C:\Users\Toan Phung\curtain_media\files\curtain_upload\0a0d33de-478b-4654-8cec-811a86400062.json"
parse_curtain_from_json... |
0a7d361c33127698b9c2d9619922cc5e5174f831c62b4227b3fee5c8ba5aca67 | Python | 983 | 34 | """The pydFC toolbox.
Submodules
---------
dfc_methods --- implementation of dFC methods
multi_analysis --- multi analysis class implementing
multiple dFC methods simultaneously
time_series --- time series class
dfc --- df... |
914a50aaa91846b38a9a9866272d1cf2da1ec1e1016107904fea85db186d8e10 | Python | 984 | 16 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
from openfl.interface.aggregation_functions.adagrad_adaptive_aggregation import (
AdagradAdaptiveAggregation,
)
from openfl.interface.aggregation_functions.adam_adaptive_aggregation import AdamAdaptiveAggregation
from openfl.interface.a... |
0a5a9ac084eda6514605a133abc0e5d1f1b9a4e181f1ccb39b6f82d8cf4a6076 | Python | 986 | 31 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Path checks tests module."""
import os
from pathlib import Path
import pytest
from openfl.utilities.path_check import is_directory_traversal
@pytest.mark.parametrize(
'directory,expected_result', [
('first_level', Fals... |
305fe353bc918624f19a65b26e4a94c38206626b6419a21e172bf209ef7393c2 | Python | 986 | 37 | """The Reinvent optimization algorithm"""
from __future__ import annotations
__all__ = ["ReinventLearning"]
import logging
from typing import TYPE_CHECKING
import numpy as np
from reinvent.models.model_factory.sample_batch import SmilesState
from .learning import Learning
if TYPE_CHECKING:
from reinvent.scorin... |
9467406a1bd9c05ca7b57420fd6daf2f054752e600ff88890cf2718816277b6a | Python | 986 | 53 | from brian2 import *
import time
from globparams import *
defaultclock.dt = 1*ms
prefs.core.default_float_dtype = float32
eqs_neurons = '''
dv/dt = (ge + rand() - v * OM_DECAY) / (1*ms) : 1
dge/dt = -ge / (1*ms) : 1
dspiked/dt = -spiked / (1*ms) : 1
'''
N = NeuronGroup(SIZE, eqs_neurons, threshold='v>VT... |
02e0d23daeb5ae32e66bfe2adbe0f9d16133cfb5366a846f18d4c447c6ee4317 | Python | 987 | 28 |
import torch
import torch.nn as nn
def get_initializer(non_linearity: str = "relu"):
non_linearity = non_linearity.lower()
if non_linearity == "selu":
# fix pytorch gain for SNN
non_linearity = "linear"
def initializer(m):
if isinstance(m, nn.Linear):
if non_linearity... |
c87026261507c595916814fc78454d18418b0ca574ce38bf8d7c399b7df21e77 | Python | 987 | 33 | import os
import glob
import paddle
from paddle.utils.cpp_extension import CppExtension, CUDAExtension, setup
def get_extensions():
root_dir = os.path.dirname(os.path.abspath(__file__))
ext_root_dir = os.path.join(root_dir, 'csrc')
sources = []
for ext_name in os.listdir(ext_root_dir):
ext_dir... |
ce83d904c7034d26efbb90c0caf4baca6fcc50452a5fc9e5492fcdc75c3439b7 | Python | 988 | 33 | import SimpleITK as sitk
import glob
import os
import platform
directory_split = "\\" if platform.system() == "Windows" else '/'
def read_itk(filename):
return sitk.ReadImage(filename)
def read_dicoms(dicom_folder):
reader = sitk.ImageSeriesReader()
dicoms = reader.GetGDCMSeriesFileNames(dicom_folder)
... |
01fd77ab60ac5df9b562f72ff95c1a6991dd6be4d3db993c8b1d7c534d63fe4f | Python | 989 | 47 | #!/usr/bin/env python
"""
Setup module for ModelAngelo
"""
import os
import sys
from setuptools import setup, find_packages
sys.path.insert(0, f"{os.path.dirname(__file__)}/model_angelo")
import model_angelo
project_root = os.path.join(os.path.realpath(os.path.dirname(__file__)), "model_angelo")
setup(
name=... |
e77039cd4f31c753dbd80ce1ab7dd28b8e0e0ea48a4c1736fa6a3ef99f01acca | Python | 989 | 28 | import torch.nn as nn
from reinvent.models.transformer.core.network.encode_decode.clones import clones
from reinvent.models.transformer.core.network.encode_decode.sublayer_connection import (
SublayerConnection,
)
class DecoderLayer(nn.Module):
"Decoder is made of self-attn, src-attn, and feed forward (defin... |
23c2a13e494a1ccddc32d7935eaebd8ef840c0cd3f9e520a5234293b9d63952a | Python | 990 | 42 | import argparse
from ase.io import iread
from nequip.utils.test import compare_neighborlists
def main():
parser = argparse.ArgumentParser(
description="Compares neighborlist implementations (ase, matscipy, vesin) on an ASE-readable file."
)
parser.add_argument(
"-fname",
help="nam... |
dfb4a271885fd672d2ce9a99e459d007744d42ccc73005e78d36f00a5d00ca53 | Python | 990 | 38 | """BrainData-specific test fixtures."""
import pytest
import numpy as np
from nltools.data import BrainData
@pytest.fixture(scope="function")
def small_brain_data_for_cv():
"""Fast fixture for CV testing: 24 samples, 10 features, 5 voxels."""
import nibabel as nib
np.random.seed(42)
spatial_shape ... |
a60d54a053a8db1d242d08affb164c13a716dbc0d99872db1bbfa35a39a40a6e | Python | 991 | 43 | import itertools as it
from typing import Iterable, Sequence, TypeVar
import more_itertools as itx
T = TypeVar("T")
def unpack(iterable: Iterable[T], default: Sequence[T]) -> Iterable[T]:
"""Return default if iterable has no elements.
Allows safe unpacking of possibly empty iterables
Parameters
--... |
ab3f0d0af45824843ba2d9607049fe59b6800a3efa1786bc144a77eaf834a587 | Python | 991 | 35 | """Config Validation"""
from typing import Optional
from pydantic import Field
from reinvent.validation import GlobalConfig
class SectionParameters(GlobalConfig):
smiles_file: str
output_csv: str = "score_results.csv"
amino_acid_library_file: str = "nnaas.csv"
smiles_column: str = "SMILES"
aa_na... |
3bdb9cb5d6fd641b43b64328b3aed012829e81c5332a5aed257d20e432c529df | Python | 992 | 29 | # Generated by Django 4.1.1 on 2022-11-23 12:32
from django.db import migrations, models
import django.db.models.deletion
import django.utils.timezone
class Migration(migrations.Migration):
dependencies = [
('celsus', '0031_curtain_file'),
]
operations = [
migrations.CreateModel(
... |
85483bd6ec498731b86decb86167d15d60c019b07db920cfc8803f44f71c660a | Python | 993 | 35 | from setuptools import find_packages, setup
setup(
name='NeuroDecode',
version='0.9dev',
author='Kyuhwa Lee, Arnaud Desvachez',
author_email='lee.kyuh@gmail.com, arnaud.desvachez@gmail.com',
license='The GNU General Public License',
url='https://github.com/fcbg-hnp/NeuroDecode/',
descriptio... |
06a5bbe4e3236cab1312b5bf1d3da6612099499e3bbe7376de663ebf81182a8c | Python | 996 | 37 | from setuptools import setup
from codecs import open
from os import path
current = path.abspath(path.dirname(__file__))
INSTALL_REQUIRES = [
'matplotlib>=3.5.1',
]
EXTRAS_REQUIRE = {}
with open(path.join(current, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='myforestplot'... |
0b1ce548322c595a9cdcd7b2640ea6d5975875fecc1e0391da8a2346c30325c5 | Python | 997 | 36 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""isort:skip_file"""
import importlib
import os
from fairseq import registry
from fairseq.criterions.fairseq_criterion import ( # noqa
... |
34f8c01cba434ede2d849482849df8ac23cc2a54e78400cd8eb6ac94a642f9b7 | Python | 997 | 25 | import pytest
import geomstats.backend as gs
from geomstats.test_cases.learning._base import BaseEstimatorTestCase
class ClusterInitializationTestCase(BaseEstimatorTestCase):
@pytest.mark.random
def test_initialization_belongs(self, n_samples, atol):
X = self.data_generator.random_point(n_points=n_sa... |
67fba83b2e306df23119c8cdc55eac00321cf4bff502b6420203d5de9d3a533c | Python | 998 | 38 | import re
from docutils import nodes
from docutils.parsers.rst import Directive
from docutils.statemachine import StringList
from sphinx.application import Sphinx
from sphinx.util.nodes import nested_parse_with_titles
from idtrackerai.start.arg_parser import get_argparser_help
class IdtrackeraiArgparser(Directive):... |
60ae4c28d43785fbb83a78458c9b996c8bd12729e78da5e96bde13c27ebcc4f6 | Python | 999 | 32 | """
Replace the data signal value with their corresponding Hilbert phase.
"""
import numpy as np
from elephant.signal_processing import hilbert
import argparse
import os
from utils.io_utils import load_neo, write_neo
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=str, required=True,
... |
8c443a6c8e15dfba46e59e3a73ab33648491a0841e72a84ffd44bcebed885627 | Python | 999 | 40 | import numpy as np
from enum import Enum, auto
from .mesh_parser import FoamMesh
def polyarea(x, y):
return 0.5 * np.abs(np.dot(x, np.roll(y, 1)) - np.dot(y, np.roll(x, 1)))
def project(points, vectors):
return np.dot(points, vectors.T)
class Parser(Enum):
POINTS = auto()
FACES = auto()
BOUNDA... |
627d55253463756818af02e09a8553d5be118178e2a4851e3c88e43728ceaf17 | Python | 1,000 | 21 | from PymoNNto.Exploration.Network_UI.Sequence_Activation_Tabs.sidebar_grammar_module import *
from PymoNNto.Exploration.Network_UI.Sequence_Activation_Tabs.sidebar_image_module import *
from PymoNNto.Exploration.Network_UI.Sequence_Activation_Tabs.reconstruction_tab import *
from PymoNNto.Exploration.Network_UI.Sequenc... |
25a6dd8ff55991e1986eda0e0043d0b555ecb515e405474883565e53f5275ad4 | Python | 1,001 | 26 | import os
import boto3
from botocore.exceptions import ClientError
from celsus.models import Curtain
s3 = boto3.resource(
service_name='s3',
aws_access_key_id=os.environ.get('AWS_ACCESS_KEY_ID', 'your-spaces-access-key-id'),
aws_secret_access_key=os.environ.get('AWS_SECRET_ACCESS_KEY', 'your-spaces-secret-... |
2b14507df6e4754c05ca8334520981494dcf6bbaa731ebaa196b074d48e6a295 | Python | 1,002 | 48 | # Copyright (C) 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
from openfl.federated.data.loader import DataLoader
class NoOpDataLoader(DataLoader):
"""No-op data loader.
This class is used when no data loader is needed.
"""
def __init__(self, **kwargs):
"""Initializes the NoOp... |
cf5a06aae562e1a59255828c54221e6b254c5fab0376cb64754c90937b6377c3 | Python | 1,002 | 39 | from PymoNNto import *
import nest
class Nest_embedding(Behavior):
def initialize(self, neurons):
# define resolution
nest.SetKernelStatus({'resolution':1.0})
# define neuron model
self.G = nest.Create(
"iaf_psc_delta", 1, params={
'E_L': 1.0,
... |
dbd036bce07ae287637e79b4afa9678d47fd19e87c1066decb267e44f2192ff3 | Python | 1,002 | 41 | #!/usr/bin/env python3
"""Update the contents of CONTRIBUTORS.txt based on .all-contributorsrc."""
from json import load
from os import chdir
from pathlib import Path
HEADER = """\
Thanks go to these wonderful people:
"""
FOOTER = """\
This project follows the [all-contributors][1] specification. Contributions of... |
124f030dad9a41a07c51eca41d7dff2791c6f044057896d07ee2a1cd5358ae3d | Python | 1,003 | 28 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
87702fabb9bfed7c50b44ba3ca3a56a1aa95ad92a4d5a295d3c9ea59bb0b9fb1 | Python | 1,003 | 37 | import torch.nn as nn
from reinvent.models.transformer.mol2mol.mol2mol import Mol2MolModel
from reinvent.models.transformer.core.network.encode_decode.model import EncoderDecoder
from reinvent.models.transformer.core.vocabulary import Vocabulary
from reinvent.models import meta_data
def _init_params(parameters):
... |
fc5c69ac6c03252c0299ff638d32366b797afb46b64d15695cd6681111aeafe2 | Python | 1,003 | 38 | # ==============================================================================
# Copyright 2023 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import jax as jn... |
45738a5c79c76be426a9d2b865e0291b712bb4f31505d716636882bd4042b9ff | Python | 1,005 | 31 | """nltools.plotting — visualization utilities for neuroimaging analysis.
`component_viewer` is the one function users call directly. Everything else
here is the drawing internal behind a data-class method — `BrainData.plot_surf`,
`Roc.plot`, `Adjacency.plot_silhouette` and friends — organized into focused
submodules:
... |
81c4fc69c428c7df57027a1287d765249b9dadc95645177abcadee857383c728 | Python | 1,005 | 30 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
e509f3b907de07f2004fc2e8d508e665d3ab0eb5fe8b530370d7c49700a829dc | Python | 1,007 | 32 | """Shared pytest fixtures for SanPy interface tests."""
import pytest
from sanpy.interface.sanpy_app import SanPyApp
from sanpy.sanpy_paths import SanPyPaths
@pytest.fixture(scope="session")
def qapp_cls(tmp_path_factory: pytest.TempPathFactory) -> type[SanPyApp]:
"""Use an isolated SanPy application for every ... |
022ec309aa9cd4cc02213aa0892bf4c4c6ec6112df001485b0c2b8bf68b0c4d3 | Python | 1,008 | 43 | from typing import TYPE_CHECKING
if TYPE_CHECKING:
from sniffles.config import SnifflesConfig
from sniffles.sv import SVCall
def get_config(*args, **kwargs) -> 'SnifflesConfig':
if '--input' not in args:
args = list(args) + ['--input', 'input.bam']
if '--vcf' not in args:
args = list... |
6770d5c823272676a492a38070a2f62f2143a0895f11e2d08ae58b8dec59c220 | Python | 1,009 | 37 | from setuptools import setup, find_packages
def readme():
with open('README.md') as f:
return f.read()
setup(name='gemmr',
version='0.4.0',
author='Markus Helmer',
url='https://github.com/murraylab/gemmr',
description='Generative Modeling of Multivariate Relationships',
long_... |
21e130153a7ef6d2a164e8190fe7c64a14ecde795a040daec05bde6f3de0e468 | Python | 1,010 | 39 | import random
from geomstats.test.data import TestData
class BaseEstimatorTestData(TestData):
MIN_RANDOM = 2
MAX_RANDOM = 5
def generate_random_data(self, marks=()):
return self.generate_tests(
[dict(n_samples=random.randint(self.MIN_RANDOM, self.MAX_RANDOM))],
marks=mark... |
4fb3887d739d342252552cad4bc47c8a87aaf5f98c2db5935f62d79a5af5de83 | Python | 1,010 | 34 | """
Merge pandas DataFrames based on the values of selected columns.
"""
import argparse
import pandas as pd
from copy import deepcopy
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='+', type=str,
help="path to input data in neo format")
CLI.add_argument("--output", nargs='?', type=... |
858205f7ff87744d4c4c54610d4e63a3e3d4778dd9c852f1925ca0f697d326df | Python | 1,011 | 26 | import geomstats.backend as gs
from geomstats.test.test_case import TestCase
class HyperbolicEmbeddingTestCase(TestCase):
def test_log_sigmoid(self, point, expected, atol):
res = self.embedding.log_sigmoid(point)
self.assertAllClose(res, expected, atol=atol)
def test_grad_log_sigmoid(self, po... |
1065ace89b39a46163ba02e58730cd38cf6ad065af9274d52aca9436bcfcc293 | Python | 1,013 | 50 | from IPython.core.display import display, HTML
from sleeprnn.common import constants
PALETTE = {
constants.RED: "#c62828",
constants.GREY: "#455a64",
constants.BLUE: "#0277bd",
constants.GREEN: "#43a047",
constants.DARK: "#1b2631",
constants.CYAN: "#00838F",
constants.PURPLE: "#8E24AA",
}
... |
7353395f2589ed40f1830a0557b7706dc68bb3d21fd28f0c0e0f59ce3b1e77ee | Python | 1,013 | 40 | import os
from pathlib import Path
def read_params_from_file(folderPath, txtFile):
"""
Loads the parameters from a txt file.
path = folder path
txtFile = file containing the params to load
"""
file = open(os.fspath(folderPath / txtFile))
params = file.read().splitlines()
file.close()
... |
98266c2f5bbebcd4e9adcf0b8a7f8a4f1f891642958ca505500bc15cb3ffa389 | Python | 1,013 | 33 | import cv2
import time
from overlay import ConfigurableOverlay, ImageOverlay
class TimestampVisualizer(ConfigurableOverlay):
default_params = {
**ConfigurableOverlay.default_params,
"time_format": "%Y-%m-%d %H:%M:%S",
"color": 255,
}
def apply(self, img, timestamp):
stime ... |
86ece9275317fd5e2bd4152ea6b8a8ccdcf296d7d8c6323a2f6d72192241d64f | Python | 1,014 | 35 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch.nn import functional as F
from torch import Tensor
import argparse
from . import register_classification_loss_fn
from .. import BaseCriteria
@register_classification_loss_fn(name="binary_cross_entropy"... |
24d0e70a1b09f287bc5cc0213f4fb669b389beb20b35f5300049c91859cf2561 | Python | 1,015 | 29 | import torch
import torch.nn as nn
from torch.autograd import Variable
class LabelSmoothing(nn.Module):
"Implement label smoothing."
def __init__(self, size, padding_idx, smoothing=0.00):
super(LabelSmoothing, self).__init__()
self.criterion = nn.KLDivLoss(size_average=False)
self.pad... |
cd9c5fdd59c11f6ae63ffc1d9a35810313e39a640714e58542a7375865c44fef | Python | 1,016 | 34 | """
Merge pandas DataFrames based on the values of selected columns.
"""
import argparse
import pandas as pd
from copy import deepcopy
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='+', type=str,
help="path to input data in neo format")
CLI.add_argument("--output", nargs='?', type=... |
ffa41ad41f59b683a1b596c911392de00781ac0935b117fe9e7f014b4b773d97 | Python | 1,016 | 21 | """Proofread the pinned structure dataset against completed current VDJdb tables.
Run via the repository environment. --fetch stages immutable hosted inputs; the
default verifies an existing local mirror. No source records or coordinates change.
"""
from pathlib import Path
import argparse
import json
from vdjdb.vali... |
aef6f80cfde65b81d51aed3bad848a91e1d7edde5dca90e4839753713d0c102c | Python | 1,018 | 32 | import argparse
import pandas as pd
import numpy as np
from keras.models import load_model
# Create an argument parser
parser = argparse.ArgumentParser(description='Load data, make predictions, and save results.')
parser.add_argument('file_name', type=str, help='Path to the data file')
args = parser.parse_args()
# L... |
8c317806c4eeb69b5339dcd0cfa2750a56e7ae2f6aff06504c3a25dfa3685265 | Python | 1,019 | 36 | from dig.ggraph.dataset import ZINC800
import shutil
def test_zinc800():
root = './dataset/ZINC800'
dataset = ZINC800(root)
assert len(dataset) == 800
assert dataset.num_features == 9
assert dataset.__repr__() == 'zinc_800_jt(800)'
assert dataset.get_split_idx() is None
assert len(da... |
b59dcf8454a65afa8983f90a4d30f3534be3810f8cc3952036b2fb87b5b9a540 | Python | 1,019 | 35 | from setuptools import setup, find_packages
with open("README.md") as f:
long_description = f.read()
setup(
name="BindsNET",
version="0.2.8",
description="Spiking neural networks for ML in Python",
license="AGPL-3.0",
long_description=long_description,
long_description_content_type="text/m... |
3ea7fb8c7f95482c1492af0b26a6d6dda700db0b8e92f8097fb8d9e89b1acaac | Python | 1,020 | 36 | """The pydFC toolbox.
Submodules
---------
dfc_methods --- implementation of dFC methods
multi_analysis --- multi analysis class implementing
multiple dFC methods simultaneously
time_series --- time series class
dfc --- df... |
4785f0db17b78476ac21e98339d2fe7b999fd8a5ef5d858f9f243b2b2fa650d2 | Python | 1,020 | 61 | # ruff: noqa: F401
from . import (
core,
core_min,
linsolver,
)
from .backend import (
ModBase,
ModNumpy,
ModTensorflow,
)
from .core import (
Array,
Domain,
Field,
MultigridField,
NeuralNet,
Problem,
State,
restrict_to_coarser,
)
from .history import (
Histo... |
5fb23be39972070b4d02f3c207f6abf5aca6bd46361f6abb543938d42a88e47e | Python | 1,020 | 34 | # ==============================================================================
# Copyright 2025 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import meshio
i... |
22bcc1e8215e81b98d00a7672d041c8090500c01f0a58c293eeab5f04f153aed | Python | 1,021 | 47 | # List of input file names
input_files = [
"CD16p_Mono.vcf",
"CL_Mono.vcf",
"CM_CD8.vcf",
"DN_B.vcf",
"EM_CD8.vcf",
"Fr_II_eTreg.vcf",
"Fr_III_T.vcf",
"Fr_I_nTreg.vcf",
"Int_Mono.vcf",
"LDG.vcf",
"mDC.vcf",
"Mem_CD4.vcf",
"Mem_CD8.vcf",
"Naive_B.vcf",
"Naive_C... |
f7429be82a7e92c35c04623c2087e8d8c870cde145a42f6bcb1cd29ccd345468 | Python | 1,021 | 45 | import experiment as exp
import schedule
import time
import arena
class TimerExperiment(exp.Experiment):
default_params = {
"interval": 1,
}
default_blocks = [
{"$num_trials": 2},
{"$num_trials": 3, "interval": 2},
{"$num_trials": 6, "interval": 0.5},
{"interval": ... |
2461e036b03b4b95747c6969eb2f41ed36b884ed187e9f8f64d6438ec85c40a2 | Python | 1,022 | 27 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import os
import nequip.nn.compile as compile_module
from nequip.nn.compile import CompileGraphModel
def test_distributed_warm_compile_gate(monkeypatch):
"""The node-parallel path must be opt-in,... |
3d6a9767e287597de4d40eede2fbfb967fb962d0dcef3bb13eebdf46af3589b2 | Python | 1,022 | 28 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
20af251927169df156776db16952cde39f6c05850bc51f0dfdd4375a2f9a1e4c | Python | 1,023 | 28 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
44afc90e9bffaa3e3f818dd24e3a340a9d9d401579a12349f6cea18212d372fd | Python | 1,023 | 32 | from setuptools import setup
from os import path
from io import open
this_directory = path.abspath(path.dirname(__file__))
def readme():
with open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
return f.read()
with open(path.join(this_directory, 'requirements.txt'), encoding='utf-8') as ... |
53bb48c9636e03a30363c2608443a9ce1364d96c1a4681dda2ce3f4d0695070c | Python | 1,023 | 40 | import tensorflow.keras.backend as K
from tensorflow.keras.losses import categorical_crossentropy
def generalized_dice(y_true, y_pred):
"""
Generalized Dice Score
https://arxiv.org/pdf/1707.03237
"""
y_true = K.reshape(y_true,shape=(-1,4))
y_pred = K.reshape(y_pred,shape=(... |
16f640ef988d3029086898dffae93e090b242aeeef4e0204ad9b04fcb6b5df1a | Python | 1,025 | 33 | """
Replace the data signal value with their corresponding Hilbert phase.
"""
import numpy as np
from elephant.signal_processing import hilbert
import argparse
import os
from utils.io_utils import load_neo, write_neo
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=str, required=True,
... |
e9b4df8201aa183baf4f32426cccedabf6d7f11f0484acdadcba181be0f7c198 | Python | 1,025 | 27 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Un... |
d5b89ba307c83859c7801859ba15e4ebf6949072812025076d374c24ee36e990 | Python | 1,026 | 32 | """Tests for canonical experimental metadata."""
import sanpy
def test_metadata_uses_canonical_keys_and_schema_defaults() -> None:
"""Keep values and presentation definitions aligned in display order."""
metadata = sanpy.MetaData()
definitions = metadata.getMetaDataDefinitions()
assert list(metadata... |
de654783232e7c478a25c33fb41b9c523abf1421b358d327ab2c70a9072e884b | Python | 1,026 | 33 | """
Replace the data signal value with their corresponding Hilbert phase.
"""
import numpy as np
from elephant.signal_processing import hilbert
import argparse
from pathlib import Path
import os
from utils.io_utils import load_neo, write_neo
CLI = argparse.ArgumentParser()
CLI.add_argument("--data", nargs='?', type=P... |
df5c5f72a8998334e08a9b3b2966ba8fc7eca1c5944465bca8aa8a32d114d00e | Python | 1,029 | 28 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
ff974bf97bdcb06ef87da43f956d78cbf104d102d525bf83d806a7013381ce27 | Python | 1,030 | 28 | from ..abstract_dataset import AbstractDataset
import os
import numpy as np
import matplotlib.pyplot as plt
class UnsteadyHeatDataset(AbstractDataset):
parametric = True
time_dependent = True
description = "Parametric heat transfer problem dataset"
data_directory = os.path.join(os.path.dirname(__file... |
636a10c47cb1f3cadf6704931a775ce946310f8ef0950ed10a15607a3e1106eb | Python | 1,031 | 28 | # Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
1027310b581ed0c2b8f2a7f51f0e18c96039162b3e6e381d3b0992eb7d78f08b | Python | 1,032 | 35 | import tensorflow as tf
import numpy as np
from PIL import Image
import os
os.sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import lattice_filter_op_loader
module = lattice_filter_op_loader.module
theta_alpha = 8.0
theta_beta = 0.125
im = Image.open('Images/input.bmp')
rgb = np.arra... |
ac7fb7a0337b5e692f36bc7839aabe027224b70e228b0c323d8872f24f0186a5 | Python | 1,033 | 34 | import geomstats.backend as gs
from geomstats.test.data import TestData
from .lie_algebra import MatrixLieAlgebraTestData
class SkewSymmetricMatricesTestData(MatrixLieAlgebraTestData):
def baker_campbell_hausdorff_with_basis_test_data(self):
return self.generate_tests([dict()])
class SkewSymmetricMatri... |
7abeb3b05eec50402c3a526de62c13f0135446159f1c71992730bdd69224a80e | Python | 1,035 | 49 | #before experiment Main code
import random
txt_size = 0.07
title_size = 0.1
image_Yloc = [-0.50,-0.2]
image_Ploc = [0.50,-0.2]
#no control offer debug version
noControl = [3,2,3]
random.shuffle(noControl)
#offer list
nc_first = [5]
nc_offer = [1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 8... |
65e33d6c4ad45781ebfa50e85a54d65b1a9c311b35140dba52306b3de6716844 | Python | 1,036 | 33 | import numpy.testing as npt
import pytest
from reinvent_plugins.components.comp_mmp import MMP, Parameters
from tests.test_data import CHEMBL4442703, CHEMBL4469449, CHEMBL4546342
from tests.test_data import CHEMBL4458766, CHEMBL4530872, CHEMBL4475647
from tests.test_data import CHEMBL4440201, CHEMBL4475970
@pytest.m... |
688cd59c7ea58a57fbcfa53e30871183f974d4d47a263a6b51540624a36b9522 | Python | 1,037 | 45 | import pingpong_test_ag as p
import numpy as n
c = p.ArdCom2(port="\\.\COM3")
c.SendChar('a')
c.Receive()
c.SendNum(13242)
c.Receive()
c.SendString('asdqwugdqwufgdwqda')
c.Receive(typeSingleIn=False)
def SC(x):
c.SendChar(x)
y = c.Receive()
return y[1]==x
#print(c.Receive())
def SBC(x):
c.SendBC... |
e320d6c0fc4e4794906838cbe7bdc335154407f3f43fed26dda4b48654b32184 | Python | 1,039 | 26 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
eedbe393d8fa12f49b81322559fbdb9be0b74a7829da56455d398d72951b5518 | Python | 1,041 | 27 | """
Trigger events sending
Triggers are used to mark event (stimulus) timings during a recording.
It supports the following types:
- Desktop native LPT ('DESKTOP')
- Commercial USB2LPT adapter ('USB2LPT')
- Software trigger ('SOFTWARE')
- Arduino trigger box ('ARDUINO')
- Mock trigger device for testing ('FAKE')
Th... |
489b39df1529deb0b626e3bbd00aaa07172868b29769846989f18003833c4db9 | Python | 1,042 | 28 | # ==============================================================================
# Copyright 2023 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import matplotli... |
586cf66a7e5c5c986607d0d76447536b5cd9822eec65d4899225f2c31ddf47cd | Python | 1,042 | 43 | from sympy import symbols
import sympy.physics.units as units
from sympy.physics.units import *
def eq_split(eq):
str=eq.replace(' ', '')
parts = []
str_buf = ''
for s in str:
if s in ['*', '/', '+', '-', '%', ':', ';', '=', '!', '(', ')', '[', ']']:
parts.append(str_buf)
... |
430ee140d221ae7d0f8ffa0110d5c64adc744175c507507eb5ddd4c5ca01b56b | Python | 1,043 | 39 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Shared test configurations for transport tests."""
import pytest
import logging
from pathlib import Path
@pytest.fixture(autouse=True)
def setup_logging():
"""Configure logging for tests."""
logging.basicConfig(l... |
a780c03b130bd4dce1fb491c0f2be7c68686c4917e9b943fadf5f24e7df1474f | Python | 1,043 | 35 | import random
from geomstats.test.data import TestData
class ForwardDifferenceTestData(TestData):
N_TIME_POINTS = random.sample(range(5, 10), 1)
trials = 1
def forward_difference_last_test_data(self):
return self.generate_random_data_with_time()
class CenteredDifferenceTestData(TestData):
... |
57af09df7d054e6254c6d9e4e2a25890979665134efd4c236897c5560a677059 | Python | 1,044 | 30 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch import nn, Tensor
from typing import Tuple, Optional
class Flatten(nn.Flatten):
"""
This layer flattens a contiguous range of dimensions into a tensor.
Args:
start_dim (Optional[int... |
640f3f2ac08e06d05f27a5426ae33aba1c5bf19a94a2a093530b451cb09db8c7 | Python | 1,046 | 34 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""openfl.experimental.workflow.utilities.resources module."""
from logging import getLogger
from subprocess import PIPE, run
logger = getLogger(__name__)
def get_number_of_gpus() -> int:
"""Returns number of NVIDIA GPUs attached to... |
d305ec0632be106b42c571dd829828a9f76fea4b1301b6f81b9b8f567c3082dc | Python | 1,046 | 46 | import pytest
from geomstats.learning.kalman_filter import (
KalmanFilter,
Localization,
LocalizationLinear,
)
from geomstats.test.parametrizers import DataBasedParametrizer
from geomstats.test_cases.learning.kalman_filter import (
KalmanFilterTestCase,
LocalizationTestCase,
NonLinearLocalizati... |
137b4e3b5d5bd8b8fbd53e595fb51d2629352f64f4477f4467645bf6e6982bb0 | Python | 1,049 | 38 | import pandas as pd
import re
import numpy as np
if __name__ == "__main__":
fullname1 = "/home/hoang/data/ANDI/Metadata/UCSFFSL51ALL_08_01_16.csv"
fullname2 = "/home/hoang/data/ANDI/tadpole_challenge/TADPOLE_D1_D2.csv"
df1 = pd.read_csv(fullname1)
df2 = pd.read_csv(fullname2)
suffix = "_UCSFFSL_02... |
57a75450d10fb30044533d4a8db870c08c4500c87454c37f773c1d7f188927c3 | Python | 1,049 | 33 | class CorgieException(Exception):
pass
class IncorrectArgumentDefinition(CorgieException):
def __init__(self, command, argument, argtype, reason=''):
self.msg = "\nCommand: {}, Argument: {} {}\n Reason: {}".format(command,
argtype, argument, reason)
super().__init__(self.msg)
... |
ea4d851e47ee9e24646e6438f04e5ce5c6db919dc2e969c0c124f6dd9b960b1e | Python | 1,049 | 33 | # Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
dcb7075973853fba281dc7c3a169be79d872c492ddc7205a48f9a4ec44916dbf | Python | 1,050 | 33 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch import nn, Tensor
from typing import Tuple
class PixelShuffle(nn.PixelShuffle):
"""
Rearranges elements in a tensor of shape :math:`(*, C \times r^2, H, W)`
to a tensor of shape :math:`(*, C... |
9173b98ccf5fbab2c2aa00376686013070fce6bcda4fbb9edd9a3ab3ef9d8f2f | Python | 1,052 | 40 | """
Haiku NN modules representing orbital functions
"""
from typing import Tuple
def _determine_n_output_orbitals(
n_up: int,
n_dn: int,
determinant_schema: str
) -> Tuple[int]:
"""
Function to determine the dimensionality of the outputted up & down MO matrix blocks given
the number of up & d... |
c7a87f04d8e32c6c0a4f61b711a58773427e92aeec015d31b66aed2b3feeb366 | Python | 1,053 | 33 | # -*- coding: utf-8 -*-
"""
Created on Wed Aug 26 14:28:11 2020
@author: Tom
"""
from keras_preprocessing.image import DataFrameIterator
import numpy as np
class DataFrameIteratorPat(DataFrameIterator):
def __init__(self, dataframe, patid_col, *args, **kwargs):
super().__init__(dataframe, *args, **k... |
0cfde31b30e1380d9cb6643ad0d6903ab5c0418928c14c221156dc552cc38172 | Python | 1,055 | 29 | import matplotlib.pyplot as plt
#overhead test: 0.001092708
labels = []
values = []
#{1: 5.002260208129883, 2: 20.522356033325195, 3: 15.061616897583008} #100 iterations
pymonnto_fast_LIF = {'Overhead':0.001092708, 'Input': 20.522356033325195/300, 'LeakyIntegrate-\nAndFire': 5.002260208129883/300, 'STDP': 15.06161689... |
f0d53ceba4964be600607383f991865f560776d2e707637e28cd4502d476bec1 | Python | 1,055 | 27 | import numpy as np
import warnings
def sensitivity(sr_grid, prior):
# prior = stimulus_pdf.dot(sr_grid)
top_lim = 1e2
specificity = np.ones_like(sr_grid) * np.inf
# specificity[:,prior > 0] = sr_grid[:,prior > 0] / prior[prior > 0]
with warnings.catch_warnings():
warnings.filterwarnings('i... |
c2d79ec72de0be9b168b5bf349ecdc9600ddf071febc7b561785763aefa753e2 | Python | 1,056 | 31 | import pytest
import unittest
import torch
from reinvent.models import LibinventAdapter, SampledSequencesDTO
from reinvent.runmodes.utils.helpers import set_torch_device
from tests.test_data import ETHANE, HEXANE, PROPANE, BUTANE
from tests.models.unit_tests.libinvent.RNN.fixtures import mocked_decorator_model
@pyt... |
0bfc3b25e3456cec923cdbed66d1e012d6ef93d92c53c366efb374f58a56ca2e | Python | 1,058 | 31 | import numpy as np
import torch
from reinvent.runmodes.RL import Learning
def get_distance_to_prior(likelihood, distance_threshold: float) -> np.ndarray:
# FIXME: the datatype should not be variable
if isinstance(likelihood, torch.Tensor):
ones = torch.ones_like(likelihood, requires_grad=False)
... |
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