sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e08406f76f3889084ebdfe56af091845b7c1b78e1099399c3fbcc45235004d0f | Python | 5,565 | 172 | import matplotlib.pyplot as plt
import numpy as np
def _enforce_ratio(goal_ratio, supx, infx, supy, infy):
"""
Computes the right value of `supx,infx,supy,infy` to obtain the desired
ratio in :func:`plot_eigs`. Ratio is defined as
::
dx = supx - infx
dy = supy - infy
max(dx,dy) ... |
cbacc17cc3e4efd2aa6f5e4ea70f3d5e3ea30ef5df35a7bfac88eaed28443934 | Python | 5,566 | 153 | from PymoNNto.Exploration.Network_UI.TabBase import *
from functools import partial
class sidebar_fast_forward_module(TabBase):
def __init__(self, step_list=[100, 1000, 5000, 15000, 30000, 50000, 70000, 100000], title='PCA'):
super().__init__(title)
self.step_list = step_list
def add_recorder... |
1ee7c690d1ad05618c4885ed53bb48ec14a45687958e8127ae7f304b41397528 | Python | 5,567 | 142 | """The regeneration driver must stay a driver.
These are the tests that keep ``regenerate.py`` free of per-family knowledge.
A family of goldens is added by dropping a module into ``targets/``, and the
value of that is entirely in what it prevents: two families added on two
branches merging without touching a line in ... |
83cf9c97fad56c230abb458cb4f9595fe45051c0c94688fafe5bb9430c1df0f4 | Python | 5,568 | 159 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from torchmetrics import Metric
from nequip.data.stats import _MeanX
class MeanAbsoluteError(_MeanX):
"""Mean absolute error."""
def __init__(self, **kwargs):
super().__i... |
95c40bc35bcefc4d8ddfd30bdb7c7b8ebfbb191c1c52255bda9348182873b813 | Python | 5,570 | 98 | from PymoNNto.Exploration.Network_UI.TabBase import *
class chain_tab(TabBase):
def __init__(self, title='Chain'):
super().__init__(title)
def add_recorder_variables(self, neuron_group, Network_UI):
return
def initialize(self, Network_UI):
if Network_UI.network['grammar_act', 0] ... |
c42d5c7247169a0139b07d38f03a940ac050dc50d3c91afef5f2e8a81d881267 | Python | 5,572 | 174 |
# -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cognitiv... |
8d2276b9170fb37ea8b011e2ce89a2a29ef5a47d9988a3fd43e1a1296dc311a4 | Python | 5,573 | 194 | """
Estimate the time our spike detection takes.
- Load an abf with lots of spikes
- loop through the number of seconds in the recording
- spike detect from 0 to i sec and calculate the time it takes
Note: the raw data for this to run is not provided in the repo. We can provide it upon request.
"""
i... |
406a7a5faf6a03065729dd5ae9da0767d8dfd2855ae5d1e8e9e1c2561736b53b | Python | 5,574 | 126 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from nequip.data import AtomicDataDict
import os
import contextlib
from typing import List, Optional, Union, Final, Callable
def dtype_from_name(name: Union[str, torch.dtype]) -> torch.dt... |
d15c828f8523a32714a5b17b76ff3ad5379838d3aa46ec1160c070a1f296bc32 | Python | 5,575 | 151 | # Copyright 2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import logging
import queue
import signal
import threading
import time
from concurrent.futures import ThreadPoolExecutor
from multiprocessing import cpu_count
import grpc
import psutil
from flwr.proto import grpcadapter_pb2_grpc
from openfl.tra... |
58687997182b5d2cda3f259496f678bc0d38d84f5a6dd0cbbe2d4a75f48c6bb7 | Python | 5,576 | 163 | import pytest
import renderapi
from test_data import (render_params,
montage_raw_tilespecs_json,
montage_parameters)
from bigfeta.qctools.CheckPointMatches import CheckPointMatches
# from bigfeta.qctools.CheckResiduals import CheckResiduals # residual has bad dep
from bigf... |
a305f54bcbc4b51a82b4662df3028b02730e784c323d8e29dd1ad7066fd5413c | Python | 5,577 | 186 | """
Utility functions for plotting
"""
import os, sys
import re
from pathlib import Path
from typing import Optional, Sequence, Union
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import seaborn as sns
from astropy.visualization import LogStretch
from ast... |
e285f21a22ea9078c08a92f6dfaca249f6197bb69ff5cce946e8b6e65556c8a6 | Python | 5,578 | 180 | import torch as T
import torch.nn as nn
from Networks.network import Network
class UNet5_decoder_teacher(Network):
def __init__(self, base, expansion):
super(UNet5_decoder_teacher, self).__init__()
self._build(base, expansion)
def forward(self, image, segbox):
layer_0, layer_1, layer_2... |
b18149442279c2315b6993e0818dc30668d968dff5a306051cba8fc90677f8f1 | Python | 5,579 | 169 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""PyTorchDataLoader module."""
from math import ceil
import numpy as np
from openfl.federated.data.loader import DataLoader
class PyTorchDataLoader(DataLoader):
"""A class used to represent a Federation Data Loader for PyTorch mod... |
ce1a7e3dca5e9f3088e0f65710280459c64b8bf42b8ef8019e1f46f71abe8c52 | Python | 5,579 | 120 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""Keys for dictionaries/AtomicData objects.
This is a seperate module to compensate for a TorchScript bug that can only recognize constants when they are accessed as attributes of an imported module.
... |
2c0b17574f0e1f20780104191fac1f9edc7341e368b23c2d82d39908662ca7e4 | Python | 5,582 | 234 | from chromadb.config import Component, System, Settings
from overrides import overrides
from threading import local
from unittest.mock import patch
import pytest
import os
import random
data = local() # use thread local just in case tests ever run in parallel
def reset() -> None:
global data
data.starts = [... |
4d53ba87219b73d15cb134f3380172d3c921b2d29ea0fa44b125e48c0f391ddd | Python | 5,583 | 161 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
import time, os, glob
from tqdm import tqdm
import numpy as np
from skimage.io import imread
import seaborn as sns
import pandas as pd
import matplotlib.pyplot as plt
from skimage.metrics import structural_simil... |
e8b16fdc2c55981a0201aab99450cf55848344758a56b8e0b4393319250fadc9 | Python | 5,584 | 176 | """Resolve and stream published DANDI NWB assets into SanPy."""
from __future__ import annotations
from collections.abc import Iterator
from contextlib import contextmanager
from dataclasses import dataclass
from typing import Any, ContextManager, Protocol
import h5py
from pynwb import NWBHDF5IO
from sanpy.fileload... |
1800644a46622d02e92b3ecc46d638922c42450c60f17167fa5a2f9b2c99f65e | Python | 5,585 | 172 | import random
import pytest
import geomstats.backend as gs
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.general_linear import SquareMatrices
from geomstats.geometry.lower_triangular_matrices import LowerTriangularMatrices
from geomstats.geometry.matrices import (
BasisRepresentationD... |
5e796db645f9cc440143f4306b49614eebc48334456a7b5aa9e2260c4f1f46db | Python | 5,589 | 154 | import sys
import time
import numpy as np
import torch
from utils import logger
from typing import Optional, Dict, Union, Any
from . import SUPPORTED_STATS
class Statistics(object):
def __init__(
self,
metric_names: Optional[list] = ["loss"],
is_master_node: Optional[bool] = False,
) ... |
eeeff39ea0ec13979abedcb57c5d76ed635e9c8e0a0586068cab03556a664308 | Python | 5,589 | 123 | """
The Kuramoto Oscillator
=======================
Here, we will introduce the `Kuramoto model <https://en.wikipedia.org/wiki/Kuramoto_model>`_,
a generic phase oscillator model with a wide range of applications [1]_.
In its simplest form, each Kuramoto oscillator is governed by a non-linear, 1st order ODE:
.. math:... |
f884dd7cfb6a6b43351b6f787f3d34069740e0ae35583d31352b4261f106b512 | Python | 5,590 | 131 |
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 10 18:14:19 2020
@author: Tom
"""
import tensorflow as tf
from tensorflow import keras as k
tf.config.list_physical_devices()
import os
#os.environ['CONDA_DLL_SEARCH_MODIFICATION_ENABLE'] = '1' # needed due to dll bug in my environment - might be unnecessary for other p... |
fcf9fed85443a5f606eea20efbef083ab20505bdab6e85641a498778c3fbe32c | Python | 5,591 | 148 | """Fixtures shared by the end-to-end contract suites.
These live here rather than in each file because two of the contract suites
need the same artefacts -- the committed anchors, the committed regression
dataset, and one multi-head model that only a fine-tuning run can produce --
and building them twice would double ... |
00d2396d844dd2e120aaf947e4385bb44db3d7918b23433784ecc6d1bb8cc5c9 | Python | 5,595 | 135 | """The Agglomerative Hierarchical Clustering (AHC) on manifolds."""
import sklearn.cluster._agglomerative as ca
from sklearn.cluster import AgglomerativeClustering
import geomstats.backend as gs
from geomstats._sklearngs.cluster._agglomerative import linkage_tree
from ._sklearn import SklearnInteropMixin
class Agg... |
b6fc71081eac4c14a7eb8269bed13974b16fabd4f2ebcd504213e043814bc361 | Python | 5,595 | 161 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import torch
from torch import nn, Tensor
import math
from typing import Optional, Tuple
from .base_layer import BaseLayer
from .dropout import Dropout
class SinusoidalPositionalEncoding(BaseLayer):
"""
T... |
e557d8033b21299a196829be11b50d0d7a714bf0efb3a0c0bfa42503073ce2d6 | Python | 5,595 | 157 | """@Author: Nicolas I. Tapia-Rivas"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import time
import numpy as np
from scipy.interpolate import interp1d
from sleeprnn.common import constants
from sleeprnn.data.dataset import Dataset
from slee... |
5c83d0051bf44afaa850ee665cc27a02b473fec656e6326b0b0cb2c15db1fb86 | Python | 5,600 | 180 | import csv
import pytest
from rdkit import Chem
from reinvent.runmodes.samplers.run_sampling import run_sampling
from reinvent.runmodes.utils.helpers import set_torch_device
# FIXME: the problem here is that we need to read this from JSON but we can use
# json_config as a parameter to a function
def check_cs... |
0011e7451b3d82f1a955eb221d009a3ab534847784bb6a361432caf4a28cbbdd | Python | 5,604 | 116 | import tensorflow as tf
from common.models.audio_core_blocks import get_ResNet28_block
from common.models.wide_resnet import get_WideResNet_block
from common.models.variational_audio_core_blocks import get_VariationalResNet28_block
from common.models.embedding_pooling import get_attention_global_pooling
from common.mo... |
b832746b6722910f70d980bdd20ffaf52dabe67a821da45db146c39fb85275c1 | Python | 5,604 | 163 | """Mol2Mol transfer learning"""
from __future__ import annotations
__all__ = ["Mol2Mol"]
import logging
import os
import torch
from torch.utils.data import DataLoader
import numpy as np
import tqdm
from .learning import Learning
import reinvent.models.transformer.core.dataset.paired_dataset as mol2mol_dataset
from... |
bff80b2edaf81a00dce5a6387d4f24d3185176572f3a69e77266d7bcd5616711 | Python | 5,609 | 122 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.Visualization.Visualization_Helper import *
class isi_tab(TabBase):
def __init__(self, title='Activity/ISI', param='output', mask_param='Input_Mask', timesteps=1000, mask_color_add=(-100, -100, -100)):
super().__init__(title)
... |
b0bfd0d675a389733ed297f85db030f779bbafdbae418d2cb978e10bb8e6fe4d | Python | 5,613 | 181 | """Tools to manage generation and interconversion of bidsapps and snakemake outputs."""
import hashlib
import json
import time
from collections import OrderedDict
from pathlib import Path, PosixPath, WindowsPath
from typing import Dict, Union
import more_itertools as itx
import yaml
from typing_extensions import Lite... |
bced415200fc2453c217db83ca1b31ee5f2a0985a0479f7612f9a15a0dfaf92b | Python | 5,614 | 194 | #!/usr/bin/env python3
import argparse
import matplotlib.pyplot as plt
import numpy as np
import odil
from odil import plotutil, printlog
def get_ref_u(t, x, args):
"""
Returns an exact solution of the equation:
u_t = u_xx
"""
t = np.array(t) * args.tmax_ref
x = np.array(x)
u = np.sin... |
e9034f85a4100631cbbd35c9d8f955514474cdd7be77e610770d8734a45cedab | Python | 5,615 | 159 | import os
import numpy as np
import requests
from collections import Counter
from rdkit import Chem
from tqdm import tqdm
from time import sleep
import logging
import matplotlib.pyplot as plt
import seaborn as sns
def seq2rat(sequence):
# dict count stores information for each sequence
dict_count = dict(Cou... |
bca66402b5d7d52acd0dd4d301b1c53d3822aa471d2e25721a722c9f25f4ab83 | Python | 5,617 | 133 | import numpy as np
from utils import load_DEAP
from sklearn.model_selection import train_test_split
from torch.utils.data import TensorDataset
import torch
from sklearn.utils import shuffle
import os
import matplotlib.pyplot as plt
DATA_DIR = "/data/DEAP/data_preprocessed_python/"
def baseline_removal(data):
""... |
53e77e9b21b91c979fde234a5dad59e3e5cc0e392328f8b7df5282967a7bd247 | Python | 5,618 | 220 | """Decorator to handle vectorization.
This abstracts the backend type.
"""
import math
import geomstats.backend as gs
from geomstats.metric_geometry.point_set import Point
def _get_max_ndim_point(*point):
"""Identify point with higher dimension.
Parameters
----------
point : array-like
Return... |
7ce535e73ce9ded2b955f8a6e7c3627d213e37994d08ffc7896deff2a028ed51 | Python | 5,620 | 143 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import logging
from openfl.experimental.workflow.interface import FLSpec, Aggregator, Collaborator
from openfl.experimental.workflow.placement import aggregator, collaborator
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(_... |
c47222ca99d0139b0baebfc4f561c335072f3b7189f4dde0ede336e51b22ed9e | Python | 5,620 | 160 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
import tensorflow as tf
import keras
from openfl.federated import KerasTaskRunner
import logging
logger = logging.getLogger(__name__)
class Keras2DUNet(KerasTaskRu... |
31ebb82ed2b1d930644b763b2325a1d443b1d072a582cbe6b938ef1c7e2ba1a2 | Python | 5,626 | 125 | import numpy as np
import matplotlib.pyplot as plt
from random_orientation_utilities import *
from orientation_reconstruction_utilities import *
from multiprocessing import Pool
import matplotlib as mpl
import statistics
#################################
# input data
#################################
eeg_lf = np.load... |
a2236440f1ae18b883bba6fcc30c4fb58863075166cc193d3980b6e1f6bbd944 | Python | 5,626 | 188 | """Matched molecular pairs"""
from __future__ import annotations
__all__ = ["MMP"]
import logging
import shlex
from io import StringIO
from typing import List
import numpy as np
import pandas as pd
from rdkit import Chem
from pydantic import Field
from pydantic.dataclasses import dataclass
from .component_results ... |
54dc7c8121c86b685d900b79a776f64d7ba955d95189dd20823e14cc485205a1 | Python | 5,628 | 127 | """J calls the junction contradicts (#681): the rule, and what it refuses."""
from __future__ import annotations
import polars as pl
from vdjdb.curate.jcalls import MIN_RUN, contradicted, report
def test_a_junction_that_ends_in_another_gene_names_it():
"""`CAVSDGNAGGTSYGKLTF` is called TRAJ47 and ends in eleven... |
65bd421c93be83e1f996b6057b955d4fd3e002dff6e9196a3e074a820b5e8885 | Python | 5,631 | 136 | """
Calculate the spatial derivative on the time-delays of the wave triggers
in each channel.
The derivative is calculated using a kernel convolution.
"""
import argparse
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from warnings import warn
from scipy.interpolate import RBFInterpolator
fro... |
bb5dd743408cc1f01649b2218df4980399549b2c9ecd1d1e607db3d004e04ef8 | Python | 5,631 | 137 | """
Calculate the spatial derivative on the time-delays of the wave triggers
in each channel.
The derivative is calculated using a kernel convolution.
"""
import argparse
from warnings import warn
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.interpolate import RBFInterpolator
fr... |
48528a4905a1e564d015086cc159c225422684c494ab416bcb706c3bbf6de6ba | Python | 5,632 | 217 | """Interpolation machinery."""
from abc import ABC, abstractmethod
import geomstats.backend as gs
class Interpolator(ABC):
"""Abstract class for interpolator."""
def __call__(self, t):
"""Interpolate data.
Parameters
----------
t : array-like, shape=[n_time]
Int... |
848f866af52580e7dfe1e6fabf51a25d3d836395f239a66618dd123beb67d445 | Python | 5,634 | 174 | '''
Alex Crits-Christoph
License: GPL3
Classifies viral metagenomic contigs using a random forest classifier built on public datasets.
'''
import sys
import numpy
import subprocess
import os
import cPickle as pickle
from sklearn.ensemble import RandomForestClassifier
from collections import defaultdict
import os.path
... |
3222c531b036903678aa190c2c1383992f851dc57a75c023654da9e6912638ef | Python | 5,638 | 147 | """Loading the committed anchors, and building the graphs they consume.
`harness.py` may not import the framework, so the two operations every
anchor-based test starts with -- read the checkpoint, turn an ase structure
into the batch the forward pass eats -- have to live somewhere else. They
live here rather than in o... |
29b54e215595a256f5db51ab4eab167f6a13cf2c1476b167c4825e771ecc8b45 | Python | 5,639 | 151 | # simpleCPP_sim.py - Directly simulates a model that
# assumes CPP slopes are generated from drift rates
#
# Copyright (C) 2022 Michael D. Nunez, <m.d.nunez@uva.nl>
#
# This program 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 ... |
0c620909e52ead04dbd9a1c3bdc26489546b3b5a251122fd26cd2b4cec7f3910 | Python | 5,640 | 149 | """Example experiment for the VLAAI model."""
import glob
import json
import logging
import os
# set gpu private
os.environ['TF_GPU_THREAD_MODE'] = 'gpu_private'
import tensorflow as tf
import numpy as np
import sys
# add base path to sys
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..'))
from task... |
9f68501cf54319ffbf3ef83f3f952392ceaeaaf4d8df809433e38ce53571db7f | Python | 5,643 | 126 | import math
import torch
from torch import Tensor
import torch.nn as nn
from torch_geometric.utils.loop import add_remaining_self_loops
from ..models.utils import subgraph
from .base_explainer import WalkBase
EPS = 1e-15
class GNN_GI(WalkBase):
r"""
An implementation of GNN-GI in
`Higher-Or... |
0cbcb6e4d78e4ced155de7bd21e156991d955cd70ffabdcac9f604a145a0c9e1 | Python | 5,648 | 135 | #### binfile_parcellation.py
# Copyright (C) 2010 R. Cameron Craddock (cameron.craddock@gmail.com)
#
# This script is a part of the pyClusterROI python toolbox for the spatially
# constrained clustering of fMRI data. It performs subject level normalized
# clustering of connectivity matrices.
#
# For more information r... |
2d54d5dfabb3771adeec212b61af003493d2f5437ce9d679622a9e8b8d30d548 | Python | 5,648 | 159 | import os
from tqdm import tqdm
import lmdb
import pickle
import torch
import numpy as np
from torch_geometric.data import Data
from rdkit import Chem
from ogb.lsc import PCQM4MDataset
from ogb.utils.features import (allowable_features, atom_to_feature_vector,
bond_to_feature_vector, atom_feature_vector_to_dict, bond_... |
0a4e6da59ca5515a19442aa9ab92e808f80239c18fa31dc37b2ef071a4a91846 | Python | 5,649 | 138 | # 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... |
bbcfc457b6b98330db9fe434a88d3f423df7cb2b4196180ddbf1e0430f6b0c3f | Python | 5,649 | 131 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.model_selection import train_test_split
from sklearn.linear_model import RidgeClassifier
from sklearn.preprocessing import StandardScaler
import matplotlib
from sklear... |
896d464eb7c484e98e71a2f6427d45f2c78c0848368530ac8ad2f3e0bcc629c8 | Python | 5,653 | 168 | '''ShuffleNet in PyTorch.
See the paper "ShuffleNet: An Extremely Efficient Convolutional Neural Network for Mobile Devices" for more details.
'''
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
def conv_bn(inp, oup, stride):
return nn.Sequential(
nn... |
4ceac08901befa1e7f8802aaef3a9f618dfd5384ae31dc8a835f294a0b2e2d7f | Python | 5,656 | 180 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 8 11:23:22 2022
@author: benozzo
"""
import numpy as np
import sklearn.metrics as metrics
import pdb
def get_idx_network_subSeparated():
idx_network = np.ones([37,1], dtype=int)
idx_lcn = [0,1,2,3]
idx_network[idx_lcn] = [[1... |
6ce3cd7971a7fb6e0101b9cab961a262a87182ab97641ee6b8f159953a197ef9 | Python | 5,661 | 170 | #
# calculation of synthetic accessibility score as described in:
#
# Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
# Peter Ertl and Ansgar Schuffenhauer
# Journal of Cheminformatics 1:8 (2009)
# http://www.jcheminf.com/content/1/1/8
#
# seve... |
971e8753af8257e7b1489b4da5ee3868c6efbb7f124c3a6e3e5702d24b09068d | Python | 5,661 | 196 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import random
import glob
import numpy as np
from scipy.spatial.distance import pdist, squareform
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from scipy.sparse.linalg import eigs
from sklearn.metrics import pairwise_distan... |
b0fc5935927c514d5a087748715f8d4f50aa8ce8b01f7125f94d2a762b54e3d7 | Python | 5,661 | 129 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
d5791c987c433144774721dbfd5ac179035962d948a30bc5689bcc0cdaeec8a5 | Python | 5,663 | 143 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import logging
pass
from openfl.experimental.workflow.interface import FLSpec, Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from openfl.experimental.workflow.placement import aggregator, collaborator... |
7604a9c2c1f6a216227f847dc43730e0ab3ad84204846fb1ec0a7b3fdf2f56f7 | Python | 5,664 | 157 | import numpy as np
import xarray as xr
from numpy.testing import assert_raises, assert_allclose
from xarray.testing import assert_allclose as assert_xr_allclose
from gemmr.sample_size.interpolation import *
from gemmr.sample_size.interpolation import proc_roots, filter_interpol_roots, _calc_n_required
import gemmr.sa... |
13bec2c403ee71ccd6298452fe2815d4f6c96d6678da3856a65ee7490aab8cf3 | Python | 5,666 | 121 | import jax
import haiku as hk
import jax.numpy as jnp
from deeperwin.model.mlp import MLP, get_activation
from deeperwin.model.attention import Attention
from deeperwin.configuration import DenseGNNConfig, MLPConfig, MessagePassingConfig
from typing import Optional
def _residual(x, x_old):
if x.shape == x_old.shap... |
73778127268b6925e81b53be8b30e09cead960786acb0461e5d99894edffb54c | Python | 5,667 | 170 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from e3nn.o3._irreps import Irreps
from e3nn.nn._gate import Gate
from e3nn.nn._normact import NormActivation
from nequip.data import AtomicDataDict
from ._graph_mixin import GraphModuleM... |
a7385ada53ae6ab34d723355d06d3ad61c048012754de22a4fbe2cd380f318d7 | Python | 5,667 | 178 | from PymoNNto.Exploration.Network_UI.TabBase import *
class info_tab(TabBase):
def add_recorder_variables(self, neuron_group, Network_UI):
return
def initialize(self, Network_UI):
Network_UI.infotabs=[]
for group in Network_UI.network.NeuronGroups:
self.make_group_tab(N... |
fa751a89341ef3d02d7e0a457ef732f3846538148eb946c1fe1cc87bd1d5d8a8 | Python | 5,670 | 148 | import numpy as np
from scipy.interpolate import RegularGridInterpolator
import nrrd
from funcs import utils
# import xmltodict
def cart2fan(Z, X, Y):
"""
Perform a coordinate transformation from Cartesian to fanbeam (polar) coordinates.
This function takes Cartesian coordinates of points in 3D space and... |
14097965095deee9884ff7cc3a6c607ffc0eb52663bcbf985a513298b54cf8c3 | Python | 5,672 | 138 | """
Calculate the spatial derivative on the time-delays of the wave triggers
in each channel.
The derivative is calculated using a kernel convolution.
"""
import argparse
from pathlib import Path
from warnings import warn
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.interpolate i... |
a0ac38b39d5bac6a969e80df5eeb64d2f1589b64658eaec89c11c2ea3ba493c9 | Python | 5,673 | 138 | """
Calculate the spatial derivative on the time-delays of the wave triggers
in each channel.
The derivative is calculated using a kernel convolution.
"""
import argparse
from pathlib import Path
from warnings import warn
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.interpolate ... |
263da8fb66ac48825c7e310ebc6514df55055e755b6ebbb46ac31da8e704f4c4 | Python | 5,675 | 129 | import warnings
warnings.filterwarnings("ignore")
# import pickle5 as pickle # this is for local run
import pickle # this is for sherlock run
import matplotlib as mpl
from utilityFunctions import *
import pandas as pd
high_res=True
parent_substitutions={
'Amyg, Amygdala': 'Middle Temporal Gyrus',
'CG, Cingula... |
895da5b2dcffad3e45c7552a23aef66406e2a9c69ce6a630d5ae7a5a9c7b0810 | Python | 5,675 | 144 | """The MACELES anchor and its two references, model and calculator.
Not part of ``--target all``: it needs the optional ``les`` package at the
commit ``requirements/les.txt`` pins, and the numbers it writes are a
property of that library as much as of this repository. Folding it into
``all`` would mean a regeneration ... |
6c17aa7c1e32698c79ec8d1b30f893ca46241971ef842731dd53df2ebe5a8d29 | Python | 5,676 | 171 | import dataclasses
from dataclasses import asdict, dataclass
from typing import Any, Optional, Tuple
from reinvent_plugins.components.synthsense.endpoints import AnyEndpoint, endpoint_from_dict
from ..add_tag import add_tag
@add_tag("__parameters")
@dataclass
class Parameters:
number_of_steps: list[Optional[int... |
ca022309213b82b7d652b871d420918cdae864568b226311176f037fa7d91132 | Python | 5,679 | 188 | """Helper functions and classes for tests
"""
import functools as ft
import itertools as it
from collections import UserDict
from pathlib import Path
from typing import Any, Callable, Dict, Iterable, List, Tuple, TypeVar, Union
import pytest
from hypothesis import HealthCheck, settings
from snakebids import bids
fro... |
b1ccc69b1e2ab5dd1b3fe3f716667f7fba72e91378bd4d8ce8433940d87da8c5 | Python | 5,681 | 170 | from typing import TYPE_CHECKING, Optional, Dict, Any, Union
from uuid import UUID
import json
if TYPE_CHECKING:
from chromadb.api import ServerAPI # noqa: F401
from chromadb.api.models.Collection import Collection # noqa: F401
class AttachedFunction:
"""Represents a function attached to a collection."... |
a3d9262ba20ef5de60f15b83e42909042cd89dcfa35a7d71ecc1e20500db9938 | Python | 5,688 | 210 | from Purkinje_morpho_1 import Purkinje_Morpho_1
from neuron import h
import multiprocessing
from Purkinje_morpho_1_number import number_ind_1
import numpy as np
import matplotlib.pyplot as plt
Hines = h.CVode()
Hines.active(0)
spines_on = 1 # switch between 0 (no spines) and 1 (spines)
stimdata = dict()
stimdata['st... |
c6c1682f5a13ec1c8797e7c7ebc276df137ae8443368a9185ebc74e57c2ca8f1 | Python | 5,689 | 274 | import pytest
from reinvent.models.transformer.core.vocabulary import SMILESTokenizer
from tests.test_data import SCAFFOLD_TO_DECORATE, WARHEAD_PAIR
@pytest.mark.parametrize(
"input, expected",
[
(
"CC(C)Cc1ccc(cc1)[C@@H](C)C(=O)O",
[
"C",
"C",
... |
867ee60d24250daf5612b817b816a332ffe5aa8fc259441bf391e25199dfbb93 | Python | 5,690 | 171 | # SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2020-2026, Christian Gaser. See LICENSE.
"""
The worked examples in docs/permutation.md, actually run.
Documentation that is not executed rots, and a worked example that does not work is
worse than none at all -- it is a trap for the one reader who trusts it. So ... |
c752c497be3ffc0d032e298d8abc19370ea482881c03dbb4ffba3a113b38e71e | Python | 5,690 | 203 |
import time
import multiprocessing as mp
from ._recorder import _Recorder
from .. import logger
from ..gui.streams import redirect_stdout_to_queue
class StreamRecorder:
"""
Class for recording the signals coming from LSL streams.
Parameters
----------
record_dir : str
The directory wher... |
6b4a88b3c55416043116c24ac4f0eeb55ba340d6c673f1afb63c716429ab734d | Python | 5,691 | 180 | # -*- coding: utf-8 -*-
import os
import random
import numpy as np
import tensorflow as tf
from sklearn.model_selection import KFold
from JSLib.JSLog import JSLog
from JSLib.JSData import JSData
from JSLib.JSModels import JSModel_MH_DSCNet
from JSLib.JSExperiment import JSExperiment
def JSCreate_Experiment(jsData,... |
ac298e928ed31a8c141ec342f95d240b8b6ec3da167ca8ff793cc2ebfce5ca10 | Python | 5,696 | 167 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Cryptography CA utilities."""
import datetime
import uuid
from typing import Tuple
from cryptography import x509
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.primitives import hashes
from cryptograp... |
d1d6db92cc36e1e7dc3cba0990c641764e4734a0deae377c3b9ebf99b4938596 | Python | 5,696 | 209 |
from sleepy.processing.dataset import Dataset
from scipy.io import loadmat, savemat
import numpy as np
class MatDataset(Dataset):
"""Implements the :class:`Dataset` interface of getters and setters. The
sleepy-properties make use of a decorator that prepares the sleepy structure
in mat-file before... |
117e4fa890b3227233335d470ce1b86e713812303c48c5f9799414d4fcfec9f6 | Python | 5,697 | 193 | import numpy as np
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.optim.lr_scheduler import StepLR,MultiStepLR
import math
import torch.nn.functional as F
from torch.utils import data
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset
from preproces... |
b6e4c6f92b969c4c050cc6834432467ea64f31dd157984d0953ef37c276679bd | Python | 5,699 | 153 | # 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... |
f9fe103fda31c58eebfc681c8a7bd74950c18ef3119b2925e9916e11d83d2321 | Python | 5,701 | 176 | from typing import Optional, Iterable, Union
import torch
from bindsnet.network import nodes
class SubtractiveResetIFNodes(nodes.Nodes):
# language=rst
"""
Layer of `integrate-and-fire (IF) neurons <https://bit.ly/2EOk6YN>` using
reset by subtraction.
"""
def __init__(
self,
... |
073903fbffcaebae55270c250f701fa62c7a8c232724e718bb5024a78c624297 | Python | 5,702 | 204 | import torch
import time
#heating up the CPU
#for i in range(1000):
# temp = np.random.rand(10000, 5000)*np.random.rand(10000, 5000)+np.random.rand(10000, 5000)
d = 'cuda'
t = torch.float64
#for i in range(60):
for i in range(1):
measurements = []
steps = 1000
#######################################... |
0eacde3de1ce5c7568a51835a41874b2511f2accbb197fb1600d4399a608488a | Python | 5,702 | 217 | """
Synapse partner assignment via neurotransmitter diffusion simulation
"""
import argparse
from sys import argv
import numpy as np
import pandas as pd
import tifffile as tif
from skimage.morphology import dilation, ball
from cloudvolume import CloudVolume
from utils import load_volume
## Fibonacci spiral model
d... |
8766dd939809de98e252e095418e8c836dfbd8278c4c78b8136531fbb8e63e0a | Python | 5,707 | 164 | """Tests for the standalone OLS helper `nltools.algorithms.regression.regress`.
`regress` is public (re-exported in `nltools.algorithms.__all__`) and tutorial-facing,
but its numeric output was previously unverified. These tests pin b/se/t/p/df
against an independent reference (`scipy.stats.linregress`) and cover the ... |
8cfe48bd724599339ff947c50006d9a1228e58f3c2c33754af9625707d5aa24c | Python | 5,711 | 133 | import gc
import torch
torch.set_num_threads(20)
from torch import nn
from torch.nn import Module, Parameter
from torch_geometric.nn import GATConv
class GNNLayer(Module):
def __init__(self, in_features, out_features, model_type='GCN'):
super(GNNLayer, self).__init__()
self.in_featu... |
6f79115ca8b2b10c51a7c192d93bc2d18b57fa0c280d023268aaf26b5e12289f | Python | 5,712 | 141 | """
Cross-Validation Data Classes
=============================
Scikit-learn compatible classes for performing various
types of cross-validation
"""
__all__ = ["KFoldStratified", "set_cv"]
__author__ = ["Luke Chang"]
__license__ = "MIT"
from sklearn.model_selection._split import _BaseKFold
from sklearn.utils.valida... |
75a4d3c4068ae0f988913dc10b1e590ee814c9f5d846b451dc09f50cd735a6f3 | Python | 5,713 | 173 | # -*- coding: utf-8 -*-
import os
import numpy as np
import logging, argparse
from data_functions import load_data, get_windows
import h5py
import matplotlib.pyplot as plt
from calc_stats_ms import *
from mpi4py import MPI
import time
import configparser
import sys
def get_feature_vector(mutation_positions, genot... |
6dc87b8657a93c049d8bfa9dcd9f88affe3f2358ac4aa257aef0df95073f2c92 | Python | 5,716 | 189 | from PymoNNto.NetworkCore.Behavior import *
import copy
class Recorder(Behavior):
initialize_last = True
visualization_module_outputs = []
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.variables = {}
def initialize(self, parent_obj):
self.add_ta... |
9c6e1548d1fa0c2325d8a1d2601ce4d556311b3d26554c9bce648401dbfed799 | Python | 5,716 | 164 | from ... import logger
CAP = {
'GTEC_16': ['TRIGGER', 'Fz', 'FC3', 'FC1', 'FCz', 'FC2', 'FC4', 'C3',
'C1', 'Cz', 'C2', 'C4', 'CP3', 'CP1', 'CPz', 'CP2', 'CP4'],
'BIOSEMI_64': ['TRIGGER',
'Fp1', 'AF7', 'AF3', 'F1', 'F3', 'F5', 'F7', 'FT7',
'FC5', 'FC3', 'F... |
26a9c1ebf9bfe23d0682f7e3bb642138e55fdb5743dd2ef92454ce041832212e | Python | 5,728 | 203 | """
Implementation of functions for Multi Analysis of dFC.
Created on Dec 3 2024
@author: Mohammad Torabi
"""
from copy import deepcopy
from joblib import Parallel, delayed
from .dfc_methods import *
################################# DATA_LOADER functions ######################################
def create_measure... |
4a53868fca80b85b17cc0f25aeb555e73f2d10c47d0dd805a41466a6f3b05834 | Python | 5,728 | 193 | import random
import pytest
from geomstats.geometry.poincare_half_space import PoincareHalfSpace
from geomstats.information_geometry.normal import (
DiagonalNormalDistributionsRandomVariable,
MultivariateNormalDistributionsRandomVariable,
NormalDistributions,
SharedMeanNormalDistributionsRandomVariabl... |
3fad1e3be544d1938174f42ff857de9c004fa8c99dae2fe1308e2fd5401f595e | Python | 5,729 | 167 | #!/usr/bin/env python
import json
import sys
from typing import List, Tuple
import pandas as pd
def check_eddy_s2v(
eddy_s2v: bool,
slspec_txt: bool,
has_slice_timing: bool,
json_file: str,
) -> None:
"""Check if slice-to-volume correction can be performed"""
if eddy_s2v and not slspec_txt:
... |
8537118ddd3809626b9e595ed065a063dc49023585d14fbfaec853daa060e50a | Python | 5,730 | 131 | """Peptide duplication must not reweight the shared TCREmp geometry."""
from __future__ import annotations
import os
import subprocess
import sys
import numpy as np
import polars as pl
import pytest
from vdjdb.motifs import tcremp as TE
def test_fit_sample_is_independent_of_process_hash_seed():
code = """
impo... |
54c3617afbaccc5a5f0e5d568b38dae7e1f6911b0eb8efb96aa228c734b84283 | Python | 5,733 | 124 | import numpy as np
import torch
from torch.utils.data import DataLoader
from metric import *
from models import *
from data import *
import argparse
import sys
import os
class Tester():
def __init__(self, smile_list, label_list, conf_tester):
self.config = conf_tester
self.smile_list = smile_list
... |
daa7e42ff5591840aa5fdc3c11c962d518711f3d1e4d1154ef89a93d85ea9786 | Python | 5,733 | 212 |
import pingouin as pg
import pandas as pd
import numpy as N
from scipy import stats as st
import statsmodels.api as sm
import statsmodels.formula.api as smf
def mixedlm(array1, array2):
mouse = N.hstack([N.ones(len(array1[d]))*d for d in range(len(array1))])
values1 = N.hstack(array1)
values2 = N.hstack(... |
5a5d0ef3c16b3e59a63c75d1f873e07261ece3a84c9daba30f61cd1ce00f8762 | Python | 5,735 | 189 | #!/usr/bin/env python3
import argparse
from pathlib import Path
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from helper_functions import (
annotate_medians_single_boxplot,
build_experiment_display_info,
canon_task,
get_default_experiment_name_map,
order_by_median_dict,... |
cf7d38d47df2608052c6c43947b95f9b4090ea770e21feb882242837922c7012 | Python | 5,736 | 171 |
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import ppafm.ml.AuxMap as aux
import ppafm.ocl.field as FFcl
import ppafm.ocl.oclUtils as oclu
import ppafm.ocl.relax as oclr
import torch
from matplotlib import cm
from ppafm.ml.Generator import InverseAFMtrainer
from ppafm.ocl.AFMulator imp... |
bdba0b2afa0e4711b2b72df0c5fca4715cd10f6c12e32e73c5bceaa9ef5056c6 | Python | 5,738 | 180 | from unittest import TestCase
import unittest
import pytest
import numpy as np
from smithers.io.openfoam import OpenFoamHandler, FoamMesh
openfoam_mesh_path = "tests/test_datasets/openfoam_mesh"
openfoam_mesh_binary_path = "tests/test_datasets/openfoam_mesh_binary"
notime_openfoam_mesh_path = "tests/test_datasets/noti... |
13989f30893bb7b77232e5a3e57a483b36051c9bfa46a9b57d99fc80e60e1545 | Python | 5,741 | 162 | from abc import ABC
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
from scipy.stats import truncnorm
# with dropout and bn
class MLP(nn.Module, ABC):
def __init__(self, input_dim, hidden_dim, output_dim, num_layers=2, dropout=0.1, bn=False):
super(MLP, self).__init__()
s... |
ec41d2f4404aaa13c9c0c923533914f97c6097d672f522adb950e5b90605ed46 | Python | 5,741 | 162 | """Load Axon Binary Format recordings."""
from typing import Any
import numpy as np
import pyabf
from pyabf.waveform import EpochTable as PyAbfEpochTable
from sanpy.fileloaders.epochTable import epochTable as SanPyEpochTable
from sanpy.fileloaders.fileLoader_base import fileLoader_base, recordingModes
from sanpy.sa... |
d1dac6af534593b8d9f0c9c53c0a4e3e62a991cdd12065193a00576d9a1b3032 | Python | 5,745 | 160 | """Regression on Manifolds/Geodesic metric spaces."""
import random
from sklearn.base import BaseEstimator
import geomstats.backend as gs
from geomstats.learning.euclidean import LinearRegression
from ._utils import _is_graph_space, _warn_max_iterations
class AACRegression(BaseEstimator):
r"""Generalized Geod... |
6a393d2b08fa9aceadc05ce01e5ea74f154183e7404c0b718bde5e815b089825 | Python | 5,747 | 163 | # 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 ... |
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