sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
160bf06b06b39945b1af22f8157c732048dcd0ad99a9ed4b11e0393b4ec77804 | Python | 6,893 | 199 | import geomstats.backend as gs
import geomstats.datasets.utils as data_utils
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.hypersphere import Hypersphere
from geomstats.geometry.landmarks import Landmarks
from geomstats.geometry.spd_matrices import SPDMatrices
from geomstats.geometry.specia... |
070dce13b4bae271c4f22bcbd592253521e7fb89e7a1733ffeec7670ecc38e69 | Python | 6,898 | 221 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
2f9f7e8b3eddeea222da54ca1142ce026e00b945de2d632d3e95c28509a899d4 | Python | 6,901 | 148 | """Rewrite with train for folder name"""
from pathlib import Path
def write_launch_file(file_path: Path, function_call_str: str):
assert not file_path.exists(), 'launch file already exists'
print(f'{file_path.stem}: {function_call_str}')
with open(file_path, 'w') as f:
f.write('#!/bin/bash \n\n')
... |
537b66bc5d88b5c32980a8f6329f54e90b15aad403bd95dc428a93f988bd8d38 | Python | 6,905 | 170 | import os
import collections
import yaml
from common.metadata_util import process_metadata
# Edit these.
PROJECT_FOLDER = '/path/to/sample-free-uncertainty-label-smoothing/'
DATA_FOLDER = '/path/to/osa_smw_dataset/'
# No need to edit these.
TFRECORDS_FOLDER = DATA_FOLDER + "/tfrecords_osa"
OUTPUT_FOLDER = PROJECT_... |
a7f89c6606883af83d4e5a18400f136223c03e4471cc7c0508d6b8685036a2ec | Python | 6,905 | 179 | """
Bar visual feedback class
Kyuhwa Lee, 2015
Swiss Federal Institute of Technology (EPFL)
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 Software Foundation, either version 3 of the License, or
(at your option) any ... |
e7fa70b5030ca93d3ba02ee05c8cb683a13518f011c358e39ca52f9f0a6688fc | Python | 6,906 | 163 | import numpy as np
import os
from captum.attr import IntegratedGradients
from captum.attr import DeepLift
# from openpyxl.worksheet.table import Table, TableStyleInfo
# from openpyxl.styles import Alignment
from nilearn import plotting,image,surface,datasets
from scipy.spatial.distance import squareform, pdist
def res... |
6087027cddd57ef490cfef824326b68b10d2d8fe6b818c85beb971b8247c969b | Python | 6,910 | 135 | # Copyright 2020 Forschungszentrum Jülich GmbH and Aix-Marseille Université
# "Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements; and to You under the Apache License, Version 2.0. "
from mpi4py import MPI
import os
import json
import time
import numpy as np
from nest_el... |
453020f80c684fc2172c09bdf3ab4047532655e0ccdbe07f69205e334afdb79d | Python | 6,915 | 193 | """Compute scores with ChemProp v2.x
Single-task model (target_column is optional):
[[component.ChemProp2.endpoint]]
name = "ChemProp Score"
weight = 0.7
param.model_path = "best.pt"
param.featurizers = ["V1RDKit2D"] # disables scaling!
param.featurizers_options = [{}]
transform.type = "reverse_sigmoid"
transform.hi... |
c3ce742c0eb6020fc4706a371562253901f6c634744b0f41508ae088681ead8e | Python | 6,918 | 209 | """Tests of the foundation-model constructors (mace_mp / mace_off / mace_omol /
mace_polar) through the ASE calculator. Everything here downloads pretrained
models (capability `network`, auto-marked by directory).
Split out of tests/test_calculator.py; the trained-from-scratch calculator
tests live in tests/workflows/... |
057a499b848fad61ab77f43070a73f8c25494378244d72c40b8eaec09b9e831a | Python | 6,920 | 169 | r"""
Delay Coupling
==============
In this tutorial, we will go through the different options you have to define delay-coupled dynamical systems in
PyRates. As an example, we will use a model of :math:`N = 2` interconnected leaky integrator units, the evolution
equations of which are given by
.. math::
\dot x... |
e36c3cb0398c453120d787f5da67ba24d28e322246a13165c1f4c0ccdf532726 | Python | 6,927 | 159 | import random
import numpy as np
def data_gen(train_img, train_mask, batch_size, flips=False, rotate=False):
'''Generator of training images and masks from an array dataset that can be non-square.
Used for CNN training.
Inputs:
train_img(3D numpy.ndarray of float32, shape = (T,Lx,Ly)): the ... |
34e5c9c9f5d286408afbf24dee5e063ccb515aa0ef6afe2e043b2db513777f57 | Python | 6,930 | 179 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import tqdm
from openfl.federated import PyTorchTaskRunner
from openfl.utilities... |
4f6fbf32c004a2970cfb47950d4f15fc7dfbf3019fee36fba6f2fdb19eb870f0 | Python | 6,933 | 192 | from plasticity.utils import generate_gaussian, standardize_coeff_init
import jax
import jax.numpy as jnp
import numpy as np
import re
def volterra_synapse_tensor(x, y, w, r):
"""
Functionality: Computes the Volterra synapse tensor for given inputs.
Inputs: x, y, w, r (floats): Inputs to the Volterra syna... |
c8c1cc5e37f71c91ee0a4bdc9439bb9ad1b82d96c3f7b31bd5a375997d3cfb56 | Python | 6,933 | 207 | import numpy as np
import pyabf
import matplotlib.pyplot as plt
import sanpy
def _demo_deltaT(abf):
"""Demonstrate delta duration."""
import matplotlib.pyplot as plt
# abf = pyabf.ABF(PATH_DATA+"/2018_04_13_0016a_original.abf")
epochTable = pyabf.waveform.EpochTable(abf, 0)
print('epochTable')
... |
71b6b39536325106e083acdbb9733d6343f18dc3fd30cd9a795e91d8eead2076 | Python | 6,948 | 107 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
e45fe1d82891c42fb6074ddef3e9135dc18ac6c0e2a29221440514f9f1e44e1c | Python | 6,948 | 219 | # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: MIT-0
"""
# Convert DiffDock's output into the same format with CASF-2016 Docking data.
The output from DiffDock is a PDB file, which contains a single chain
representing the pose of the small molecule ligand.
Example usag... |
ce7f82e5f011e896f5972881a19691c8996a18c9ee37e4da73e80591b8025a3c | Python | 6,949 | 208 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from .base_cls import BaseEncoder
import os
import importlib
import argparse
from utils.download_utils import get_local_path
from utils import logger
from utils.common_utils import check_frozen_norm_layer
from util... |
ca32c7a3b0ad05e6e3e532943fd1f2c8f9e46612ce1cb2d87c600616e15b3971 | Python | 6,954 | 182 | """Methods to compute feature attributions.
Compute:
SHAP
Integrated Gradients
LIME
Gradient
SmoothGrad
"""
from typing import Callable, Optional, List
import numpy as np
import shap as third_party_shap
import tensorflow as tf
def shap(model: Callable[[np.ndarray], np.ndarray],
example: np.ndarray,
... |
6afff89d3d7e21a431f4bf7112160f3e2e246150ee961ef63593cee19ba11ce1 | Python | 6,959 | 154 | # Author: Youzhi Luo (yzluo@tamu.edu)
# Updated by: Anmol Anand (aanand@tamu.edu)
import torch
import random
import torch.nn.functional as F
from torch.distributions.bernoulli import Bernoulli
from torch_geometric.data import Data
from torch_geometric.utils.dropout import filter_adj
from torch_geometric.utils.num_node... |
ce963485be92bb8dfad1cde8143cd86151c4baf293d0d8c2c9db040afeec8291 | Python | 6,959 | 213 | # convert VOC xml to COCO format json
import xml.etree.ElementTree as ET
import os
import json
import argparse
# create and init coco json, img set, and class set
def init_json():
# create coco json
coco = dict()
coco['images'] = []
coco['type'] = 'instances'
coco['annotations'] = []
coco['cat... |
fef278bf0cac266d66b80022964622ea77a7c8f70195de447ee37cfb9b53f5e5 | Python | 6,960 | 226 | # copyright (c) 2021 PaddlePaddle Authors. All Rights Reserve.
#
# 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... |
403d72fd839ceadc94ae4b875b4acb9865f8a0a243794adac192c4e2a024b002 | Python | 6,967 | 210 | """`info_keys` and `MACECalculator.check_state`.
Two parts of the calculator's contract that nothing exercised.
`info_keys` maps a PROPERTY NAME to the `atoms.info` key it is read from, the same
direction as `arrays_keys` (see tests/unit/test_calculator_charges_key.py). Its
default is not empty, so a caller who overr... |
6345bc3ace562606e99e8276b0da30961aeb721cf86aa2512ba3066729024ad7 | Python | 6,968 | 195 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Aggregator tests module."""
from unittest import mock
import pytest
from openfl.component import aggregator
from openfl.component.assigner import Assigner
from openfl.protocols import base_pb2
from openfl.utilities import TaskResult... |
55a731583a12b321f544d1606b9cc1c1f52dc87f49ec1f20d9003376e7e67d6b | Python | 6,974 | 220 | import io
from contextlib import redirect_stdout, redirect_stderr
from queue import Queue
import pytest
from hnn_core import Network
from hnn_core.mpi_child import MPISimulation, _str_to_net
from hnn_core.parallel_backends import (
_gather_trial_data,
_process_child_data,
_echo_child_output,
_get_data... |
a51feb5ef363e7e74b6722c40660d86a5205dfb53ee235a6b7a753a86b37145a | Python | 6,974 | 182 | import shutil
from dig.sslgraph.dataset import get_dataset
def test_get_dataset():
## semisupervised
# NCI1
root = './dataset/TUDataset'
dataset, dataset_pretrain = get_dataset(name='NCI1', task='semisupervised', feat_str='deg+odeg100', root=root)
assert len(dataset) == 4110
assert len(dataset... |
9f5e76de9c5acce066f16864cc20456a158d6774aac3e63b03d86bfd249ac1ff | Python | 6,976 | 201 | import numpy as np
import torch as T
from monai.data import (DataLoader, Dataset)
from monai.metrics import compute_meandice
from monai.transforms import (
AddChanneld,
Compose,
LoadImaged,
NormalizeIntensityd,
ToTensord,
Resized,
RandFlipd,
RandRotate90d,
ThresholdIntensityd,
Sc... |
ab5cec7e850b23bdb2bd1e70a2fa8ffda722c19687adb0042eb638329179cd54 | Python | 6,976 | 209 | import logging
import os
from pathlib import Path
import pytest
from qtpy import QtCore, QtWidgets
from sanpy.interface import sanpy_app, sanpy_info_widget
from sanpy import sanpyLogger
from sanpy.sanpy_paths import SanPyPaths
def test_logger_text_combines_retained_logs(
monkeypatch: pytest.MonkeyPatch, tmp_pat... |
2e1207dbf5e2549839ab5fab8804fa729bc40e090e751b01f2a4993f7765cb18 | Python | 6,981 | 186 | """Sphinx directives that read the field registry at doc-build time.
.. vdjdb-schema:: vdjdb
:columns: name, title, comment
.. vdjdb-vocabulary:: species
.. vdjdb-score-rules::
**There is no generated ``.rst`` in the tree, and that is the whole point.** A column table written
out by a script is c... |
810170c0e5a07da3fc4db0f4ea2a7a330c361e940c35bff815787e530dafe7b3 | Python | 6,984 | 261 | import pandas as pd
from uniprotparser.betaparser import UniprotSequence
curtain_ptm_de_form = {
"_reverseFoldChange": False,
"_comparisonSelect": "",
"_comparison": "",
"_primaryIDs": "",
"_geneNames": "",
"_foldChange": "",
"_transformFC": False,
"_significant": "",
"_transformSig... |
dab9dd200ead559ea2ba1b4d57c094edfb1b00dc6751c01aa0ebbda773878d27 | Python | 6,990 | 235 | # this is the same script as before but we use more data.
import numpy as np
import matplotlib.pyplot as plt
import torch
import h5py
import torch.nn as nn
from torch.utils import data
# number of available gpu
ngpu = 1
batch_size = 128
decayRate = 0.95
lr = 0.001
dataRoot = "../../data"
# this is a for loop to l... |
b4f0017ec822a3ee9d2e8118092637e887d49da641385c97aef1e199828d6935 | Python | 6,991 | 249 | #!/usr/bin/env python3
import argparse
import pickle
import numpy as np
import odil
from odil import printlog
from odil.runtime import tf
def get_exact(args, t, x):
t = tf.Variable(t)
x = tf.Variable(x)
u = tf.zeros_like(x)
with tf.GradientTape() as tape:
ii = [1, 2, 3, 4, 5]
for i ... |
f2dcc47405ac15781c205baf0a7fc0c35864ed924411e0b01a1723d1cb8c24ce | Python | 6,992 | 204 | """Tests for the frozen structural `PredictResult` result record.
The spec's shape table (`development/specs/braindata.md`, "Prediction and
decoding") is the contract: one record class, a required ``spatial_scale``
discriminator, and exactly one legal field combination per spatial scale.
"""
from dataclasses import F... |
2867d0b8815acc0d4ca25a6b64c08dc9aa912f7d8452c8dba4cb1badcde67d40 | Python | 6,997 | 171 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
from typing import Any, Dict, List, Optional
import torch
from e3nn.o3._irreps import Irreps
from e3nn.o3._spherical_harmonics import SphericalHarmonics
from nequip.data import AtomicDataDict
from ne... |
3578afe0dea77cfdebc60b04128399a03461da5e9574f5e9c88dabc868a541ff | Python | 6,997 | 159 | import torch.nn as nn
from .contrastive import Contrastive
from dig.sslgraph.method.contrastive.views_fn import Diffusion, DiffusionWithSample
class MVGRL_enc(nn.Module):
# MVGRL includes projection heads and combines two views and
# encoders when inferencing graph-level representation.
def __init__(sel... |
33beb15cae5533f08e12356a39da0a8b9ffa1366770329faa6c9d34aeff6b2ea | Python | 7,006 | 177 | # 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.
import math
import torch
import torch.nn.functional as F
from fairseq import metrics, utils
from fairseq.criterions import FairseqCriterion, ... |
791f612b55d436c43bda4c93e17a5c04c9394456d5952703e8890d9c7ab521d2 | Python | 7,007 | 129 | import os
import torch
import numpy as np
from .model import SphGen
class G_SphereNet():
r"""
The method class for G-SphereNet algorithm proposed in the paper `An Autoregressive Flow Model for 3D Molecular Geometry Generation from Scratch <https://openreview.net/forum?id=C03Ajc-NS5W>`_.
This cla... |
cbc2a0737a8dfbb9f2132957de3ec004d7a597e15a0a87ec2bb86c68baadf63a | Python | 7,014 | 235 | from datetime import timedelta as t
import numpy as np
from sklearn import preprocessing, feature_selection, svm, metrics
import pandas
def splitting(data_list, datetimes_list, seizure_info_list, n_seizures_train):
data = {}
datetimes = {}
seizure_info = {}
# Train
data['tra... |
55ac00fc99e408e7e91fa5eeea4e6c3f7401a888653d5b798d1b60b3ab8fb920 | Python | 7,023 | 197 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
This file contains utility functions for Secure Aggregation's cipher related
operations.
"""
import random
from typing import Union
import numpy as np
from Crypto.Cipher import AES # nosec B413
from Crypto.Util.Padding import pad # ... |
eaf1a9d1008c5500a69eb26ec95acad47c6a8935977fa0ee54e0f898d4355acf | Python | 7,025 | 203 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Implementation of FedCurv algorithm."""
from copy import deepcopy
import torch
import torch.nn.functional as F
def register_buffer(module: torch.nn.Module, name: str, value: torch.Tensor):
"""Add a buffer to a module.
Args:
... |
ec2b3807b58ea51c6877d3ca94de63eda5db4397eeb7b6227f4e6ef87c889d13 | Python | 7,025 | 216 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Workspace utils module."""
import logging
import os
import shutil
import sys
import time
from contextlib import contextmanager
from pathlib import Path
from subprocess import check_call # nosec
from sys import executable
from typing imp... |
536c3447f67db95e45be95aa8c173ba2ac5b3ca73aeaa8d3288ecbc300733912 | Python | 7,029 | 224 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates 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 C... |
78f355e8cd5c453fae6ddfd71202c37e5afb32795753a2ccbda2e9df43f8f001 | Python | 7,036 | 148 | import haiku as hk
import jax
import numpy as np
from jax import numpy as jnp
from deeperwin.configuration import EnvelopeOrbitalsConfig, MLPConfig
from deeperwin.model import WavefunctionDefinition, MLP
from deeperwin.model.orbitals.utils import _determine_n_output_orbitals, _determine_elec_idxs
from kfac_jax import ... |
0ea9dff7aedd8b72c0975993015ce6a64042236404f4c5f9142f7bbdedae6bcc | Python | 7,041 | 218 | """Tests for constructing an ``analysisDir`` from stable test data."""
from pathlib import Path
from unittest.mock import MagicMock
import pandas as pd
import pytest
import sanpy
def test_dir(test_data_dir: Path) -> None:
"""Discover supported recordings in the test data directory.
Args:
test_data... |
cafecb029d5a85551f7b486ab65555b05c0e3605916e72e1f49c262df1dfa1af | Python | 7,042 | 199 | # 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."""
from collections.abc import Iterable
from logging import getLogger
from os import makedirs
from pathlib import Path
from urllib.request import urlretrieve
from zipfil... |
627d987896fcadf93a308d6b6834b4d16b718fc7938b5f61525b7d1f0a96cabe | Python | 7,045 | 198 | # Authors: Mainak Jas <mainakjas@gmail.com>
# Blake Caldwell <blake_caldwell@brown.edu>
import json
from pathlib import Path
from urllib.request import urlretrieve
import pytest
import hnn_core
from hnn_core import read_params, Params, convert_to_json
from hnn_core.hnn_io import read_network_configuration
f... |
a1343cae2ab4d94b37bbfb39f2707df856eab541b406432cbc35cc8a02f32281 | Python | 7,045 | 196 | """Tests for MACE-MDP (AtomicDielectricMACE) fine-tuning support.
Covers:
- test_mdp_finetune_updates_params: verifies that a short fine-tuning run
completes without error and that at least some model parameters change.
- test_mdp_finetune_wrong_model_type_raises: verifies that passing a non-MDP
model type... |
78ceb6e8f101d9ab0b021807aee136e40fc3f46d4f48b7cbb1efde2dcac0966f | Python | 7,046 | 147 | from PyQt5 import QtCore, QtWidgets
from PyQt5.QtCore import QRect, QSize
from PyQt5.QtWidgets import (QWidget, QCheckBox, QLabel, QComboBox,
QPushButton, QSpinBox, QDoubleSpinBox,
QFrame, QLineEdit, QTableWidget, QStatusBar)
from ._scope import _BUFFER_DURATIO... |
b820ec8298990ca808b4f9de18ae9906dabd1529284688d5a4a280203a3c9eaf | Python | 7,046 | 197 | # Method signatures differ between Qt bindings, so overrides can't match them all
# pyright: reportIncompatibleMethodOverride=false
import logging
from collections.abc import Callable
from qtpy.QtCore import Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtCore import QEvent, QSize, Qt, QTimer
from qtpy.Qt... |
2829992c4f3cb03c6af4d5979f55c18cdc3cb91fd91d03303f4dc733004541c3 | Python | 7,051 | 208 | from sklearn.cluster import BisectingKMeans, AgglomerativeClustering, KMeans, DBSCAN
from sklearn.model_selection import KFold
from umap import UMAP
import numpy as np
import pandas as pd
def umap_cluster(data, z_score=False, n_clusters=None, umap_params_in=None, cluster_params_in=None, random_state=999):
"""
... |
57e306cfd1cc14f61d2903b11829867c30451fab36c99dcc0714e1d723561612 | Python | 7,053 | 199 | """
Detect and characterize critical points in the optical flow vector field at each
time point.
"""
import argparse
import numpy as np
import neo
import matplotlib.pyplot as plt
from shapely.geometry import LineString
from utils.io_utils import load_neo, write_neo, save_plot
from utils.neo_utils import analogsignal_t... |
6567c70e747a8cf5f5b7531739fb71d524b8ddb9c92388186396ad3ecc46bbfc | Python | 7,058 | 200 | """
Detect and characterize critical points in the optical flow vector field at each
time point.
"""
import argparse
from pathlib import Path
import numpy as np
import neo
import matplotlib.pyplot as plt
from shapely.geometry import LineString
from utils.io_utils import load_neo, write_neo, save_plot
from utils.neo_ut... |
bfe27d520e673552d44f7452b9a0cdef4755bb78e99d76d8384dcd79a632c461 | Python | 7,059 | 199 | """
Detect and characterize critical points in the optical flow vector field at each
time point.
"""
import argparse
import numpy as np
import neo
import matplotlib.pyplot as plt
from shapely.geometry import LineString
from utils.io_utils import load_neo, write_neo, save_plot
from utils.neo_utils import analogsignal_t... |
e880115bbceea1decb9d02a33c629f94151d3e2c7a45c4ca779b6bed72727d00 | Python | 7,060 | 156 | """
Determine the threshold between Up and Down states for each channel
by fitting the respective amplitude distributions.
"""
import numpy as np
import argparse
import os
import scipy as sc
import warnings
from scipy.optimize import OptimizeWarning
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, ... |
bd62119ff8239958b785497cbe97c85f1f9e4f114b554ae7436a3e51a3ecbef9 | Python | 7,063 | 187 | from PymoNNto.Exploration.Evolution.common_UI import *
from PymoNNto.Exploration.Evolution.PlotQTObjects import *
from PymoNNto.Exploration.Network_UI.Basic_Tabs.Helper.syntax import *
class Execute_UI(Execution_Manager_UI_Base):
def get_folder(self):
return 'Plot_Project_Clones'
def get_title(self):... |
2ee52b0dd201c764bd136e4173c87bc6e4d2109aff4f9454f334387c632418e0 | Python | 7,064 | 318 | # %% [markdown]
# # Preamble
# %%
import numpy as np
from joblib import Memory
import dgamem.grid as dga
import dgamem.grid_ref as ref
memory = Memory("data/cache")
# %% [markdown]
# # System
# %%
shape = (80, 80) # grid shape
size = 80**2 # number of states
temperature = 0.5
sep = 0.05 # grid spacing
area = se... |
b946600b8ba37e51c23ac23578022f384e208403d6e20292f3a711bc26f9cb22 | Python | 7,065 | 170 | r"""
Delay Coupling
==============
In this tutorial, we will go through the different options you have to define delay-coupled dynamical systems in
PyRates. As an example, we will use a model of :math:`N = 2` interconnected leaky integrator units, the evolution
equations of which are given by
.. math::
\dot x... |
5f77cb45afe0f5e8d6a2dda68db8358cc28eeb6c427a15a1c42571fd057df3e2 | Python | 7,069 | 210 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft
# Licensed under the MIT License.
# Written by Bin Xiao (Bin.Xiao@microsoft.com)
# Modified by Ke Sun (sunk@mail.ustc.edu.cn)
# ------------------------------------------------------------------------------
from ... |
4c6d0c2d25a5098b2ff7165b5f79ccc9ac2f173ee4d749daacb73ae6135a97b1 | Python | 7,070 | 228 | import numpy as np
import torch
import torch.nn as nn
import progressbar
import time
import copy
def initialization(init_method, W, is_tensor=True):
""" Initializes the provided tensor.
Parameters:
-----------
* init_method : str (default = 'glorot_uniform')
Initialization method to use.... |
458ea6ba28b608fd15250e633c803a8c0fc6b7b4ae8adddef1761c93131bbc58 | Python | 7,072 | 135 | """Queries use a reference fit and its retained DBSCAN cores without changing either."""
from __future__ import annotations
import numpy as np
import polars as pl
import pytest
from vdjdb.motifs import tcremp as TE
def rows(sequences, epitopes=None):
n = len(sequences)
return pl.DataFrame({"species": ["Homo... |
25673417c4199cd5622fe249933c68c306af7ffc91d7a40a3d9fbba79b48fb81 | Python | 7,073 | 192 | import utils
import train
import torch
from torch.utils.data import DataLoader
import math
import database
import load_save
import random
import argparse
import Networks
functions_nn = {'gru2_bohb': Networks.gru2_bohb.gru,
'gru_bohb': Networks.gru_bohb.gru}
def init_all(model):
for p in model.par... |
443480a63232ad089547a652b723b2e36bec145fbb24033d03172d7c83395942 | Python | 7,074 | 184 | import tdt
import time
import os
import numpy as np
from scipy.signal import butter,filtfilt
import matplotlib.pyplot as plt
def get_online_api(config):
"""Function for returning the desired online API"""
if config.online_api == 'synapse':
return SynapseAPI()
else:
raise NotImplementedErr... |
9ae5435c06f1454feace9b42c3ee103ddb180256426b93e603feb7b9be3d7392 | Python | 7,076 | 221 | import logging
import os
from pathlib import Path
from typing import Any, List, Optional, Union
import torch
from torch.utils.data import ConcatDataset
from mace import data
from mace.tools.scripts_utils import check_path_ase_read
from mace.tools.torch_geometric.dataset import Dataset
from mace.tools.utils import Ato... |
0f1da985298370d7e5c596cddbadbabfef981f1c8c3e8c81bf72968d76b31f38 | Python | 7,077 | 218 | import numpy as np
import xlsxwriter as xw
import pickle
from aux_fun import get_selected_features
# --- Creates an xlsx file with the training results of approach A ---
def save_train_results_A(general_information, train_information, approach):
# Create xlsx
path = f'Results/{approach}/Train_r... |
6959bff6c23ec6b866ee44d430c4606862988b1d7bcae3d623ab6d4e6fbb78c3 | Python | 7,078 | 207 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import torch
from torch import nn, Tensor
from typing import Optional, Tuple
from torch.nn import functional as F
from utils import logger
from .base_layer import BaseLayer
from .linear_layer import LinearLayer
fr... |
20678dfcb9a4ce9ed5f5f302c9d0b33734bf13924469a5c560484b3ebae1009e | Python | 7,080 | 200 | """
Detect and characterize critical points in the optical flow vector field at each
time point.
"""
import argparse
from pathlib import Path
import numpy as np
import neo
import matplotlib.pyplot as plt
from shapely.geometry import LineString
from utils.io_utils import load_neo, write_neo, save_plot
from utils.neo_ut... |
cb7a124e3873d663c39f0f0a7dc774f75ebc773ac48f063c730bb364583fc075 | Python | 7,083 | 198 | import random, csv, pickle
import numpy as np
import rdkit.Chem as Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
import logging, os
def get_splitted(path):
if path is None or not os.path.isfile(path):
return None, None
smile_list, label_list = read_data(path)
X = np.array(smile_lis... |
3282347ad2569a44cbc44602417e7fe760a190cbf24484b34baa8389a995a7b2 | Python | 7,084 | 156 | """w
Determine the threshold between Up and Down states for each channel
by fitting the respective amplitude distributions.
"""
import numpy as np
import argparse
import os
import scipy as sc
import warnings
from scipy.optimize import OptimizeWarning
import matplotlib.pyplot as plt
from utils.io_utils import load_neo,... |
c1b8ccfe1f7c40f04c2bd0c4351d41f052f2f726dd618801cb7fe5d1ef848e63 | Python | 7,085 | 114 |
import time
import numpy as np
def get_configs(parser):
# Parse commandline arguments
parser.add_argument("--data_dir", default='hyper_dti/data/', type=str, help='Path to data directory.')
parser.add_argument("--name", default='run', type=str, help='Experiment name.')
parser.add_argument("--wandb_us... |
fa34072a120e973efc5bfbac5cf61a610d85b66b588a5da01e567890ddd0dadb | Python | 7,087 | 168 | # 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... |
8a5b3e9faf4ce31315a711df94117e225a80ffe63e68b09b67e2c795e15eb141 | Python | 7,088 | 157 | """
Determine the threshold between Up and Down states for each channel
by fitting the respective amplitude distributions.
"""
import numpy as np
import argparse
from pathlib import Path
import os
import scipy as sc
import warnings
from scipy.optimize import OptimizeWarning
import matplotlib.pyplot as plt
from utils.i... |
64c2e27c57b2c3b51147b9bbb7c141f5d24d6523d761ad0aff5c1c7b55f4e01b | Python | 7,094 | 235 | """
Generic utilities for online analysis.
"""
import asyncio
import functools
import logging
import os
from pathlib import Path
import time
from datetime import datetime
from glob import glob
import json
import warnings
import numpy as np
import pandas as pd
import scipy.io as sio
from ScanImageTiffReader import Sca... |
cd1063dc3b07a3fb3ea18fbb746fc931f6763de43bdbcb1d9e592e7be99df2ef | Python | 7,096 | 188 | # 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.
from typing import Dict, List, Optional, Tuple
import torch
import torch.nn as nn
from torch import Tensor
from fairseq import utils
from fa... |
fd4f16cb3258fa25a38316ea65d8d188b88b37cd137ddbc1a524520d0baab981 | Python | 7,096 | 208 | import os
import cv2
import numpy as np
import tensorflow as tf
### importing required packages
import pathlib
from PIL import Image
import matplotlib.pyplot as plt
from skimage import io
from sklearn.metrics import precision_score
from sklearn.metrics import recall_score
from sklearn.metrics import confusio... |
cd81d7e8de8455c353a0a0f6a5969bb84102ac6cb42a3e660bda17def3f70b35 | Python | 7,097 | 220 | from neuron import h, load_mechanisms
from neuron.units import ms, mV
import numpy as np
import os
import sys
load_mechanisms(os.path.dirname(__file__)+'./detector/')
# initialisation MPI
h.nrnmpi_init()
# define dt for the simulation
h.dt = 0.1
print("############### dt", h.dt); sys.stdout.flush()
pc = h.ParallelCont... |
ff9d7b246f0173e2e1c1a49a483b394e5ab06425f194d681769d821a4ece2869 | Python | 7,098 | 220 | # -*- coding: utf-8 -*-
import h5py
import numpy as np
from collections import deque
import copy
import random
import torch
import os, sys
import glob
from scipy.spatial.distance import squareform
from data_functions import load_data_dros
import pickle
from sklearn.neighbors import kneighbors_graph
class H5DisDat... |
5e5e2fe8995d0f7b4faaa2f8d9eccf3ed5b617c1ed8e784b9b963a15e8b2f81d | Python | 7,103 | 163 | #!/usr/bin/env python
#############################################################################
##
## Copyright (C) 2017 Hans-Peter Jansen <hpj@urpla.net>
## Copyright (C) 2016 The Qt Company Ltd.
##
## This file is part of the examples of the Qt Toolkit.
##
## $QT_BEGIN_LICENSE:BSD$
## Commercial License Usage
##... |
6d892bb957cf07fa00d0e27bf2e4489ae4b380238b544a02b8c075fb5cfc21d7 | Python | 7,107 | 184 | import pytest
from chromadb.config import DEFAULT_DATABASE, DEFAULT_TENANT
from chromadb.test.conftest import ClientFactories
from chromadb.errors import InvalidArgumentError
from chromadb.api.types import GetResult
from typing import Dict, Any
import numpy as np
def test_database_tenant_collections(client_factories:... |
6f53f5b877d69e2b96236d6b428ebe3f642567b6704c8337b69b3ef290303fae | Python | 7,108 | 179 | import pandas as pd
from Bio import SeqIO
import numpy as np
import tensorflow as tf
import os, subprocess, shutil
from itertools import product
class Seq:
def __init__(self, fasta_dir, encoding, k):
self.fasta_dir = fasta_dir
fasta_files = [fasta_dir + file for file in os.listdir(fasta_dir)]
... |
a6144ad8594dc8c6cb42f5a8324947302a40b015b5f389007dabdcaab0161a4d | Python | 7,114 | 224 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import numpy as np
from vedo.utils import sort_by_column
from scipy import signal
#################################################################################
class Limb:
def __init__(self, source="", author="unknown"):
self.author = author.lo... |
4e4c6fdf03e8d4d8890c18b60a591d36c2d1e68710ce88b470f3a91a3c99f096 | Python | 7,117 | 135 | """Antigen nomenclature patches.
``patches/antigen_epitope_species_gene.dict`` maps an epitope to its canonical parent gene and
species. The legacy build applied it per chunk with ``chunk_df.T.apply`` -- transpose, then a
Python call per row; it is one join here.
Coverage, measured: the dictionary covers 245 epitopes... |
5245e24cce3ff45ae0e58065de12f595adaf3ec08182f80bf3622ead6eac0a41 | Python | 7,117 | 205 | """Invariant metric test data.
Given the slowness of these tests, I've decided to separate the data that
computes a method at identity (because the normal tests will call those
methods). Just use such data if interested in more detailed tests (notice
the tests are already defined).
"""
import geomstats.backend as gs
... |
3398ef306cbf1e9bdbe6c4127a3766a6ee7bb21dbf0ef95f6181e2df67120b14 | Python | 7,128 | 198 | # -*- coding: utf-8 -*-
"""
Created on Thu Apr 22 14:27:39 2021
@author: nicol
"""
import os, glob, tqdm
from skimage.io import imread, imsave
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import rc
import matplotlib as mpl
from skimage.metrics import normalized_root_mse as nrmse
import scipy.ndi... |
7c1a689e01b9c0511876712c9bde56323d6f12092c25abcafd4ab159ab9ac41c | Python | 7,129 | 179 | import pathlib
import numpy as np
from openeye import oechem, oeomega, oeshape, oequacpac
from typing import Optional, List
class ROCSOverlay:
"""
This class contains all methods needed for running OpenEye ROCS
based on the OE python API. Env variable "OE_LICENSE" must be set
before running this code.... |
7b230bc23ad239eef03122d7700d1276233e13bff7e055bfe4fe30675d0f43b2 | Python | 7,130 | 157 | import logging
import os
import pickle
import re
import ruamel.yaml
from deeperwin.configuration import Configuration, build_flattend_dict, CheckpointConfig, ConfigBaseclass, PhisNetModelConfig
from deeperwin.mcmc import MCMCState
import jax
import numpy as np
import haiku as hk
import zipfile
from dataclasses import... |
5c2c3bcf5155578512f8863cd99a819d55747a7a208a94f1d6e6f2b515eb1d9c | Python | 7,131 | 177 | import numpy as np
from sklearn.decomposition import PCA
from jPCA.util import ensure_datas_is_list, preprocess
from jPCA.regression import skew_sym_regress
__all__ = ['JPCA']
class JPCA:
def __init__(self, num_jpcs=2):
assert num_jpcs % 2 == 0, "num_jpcs must be an even number."
self.num_jpcs =... |
8d206bc80aa617df618e1cd42c74d9d1c6be50d715e6d038065640e827ca7417 | Python | 7,138 | 132 | """The ProductPositiveRealsAndComplexPoincareDisks manifold.
The ProductPositiveRealsAndComplexPoincareDisks manifold is defined as a
product manifold of the positive reals manifold and (n-1) complex Poincaré disks.
The positive reals and complex Poincaré disks product has a product metric.
The product metric on the p... |
a458cb57520783cd76d39f1b9e94b78ad268486ddaef4f412609538f6e3c7e76 | Python | 7,141 | 167 | """
NeuroLearn File Reading Tools
=============================
"""
__all__ = ["onsets_to_dm"]
__author__ = ["Eshin Jolly"]
__license__ = "MIT"
import pandas as pd
import numpy as np
from nltools.data import Design_Matrix
import warnings
from pathlib import Path
def onsets_to_dm(
F,
sampling_freq,
run_... |
c115045843b844119aff508498c65627b2e97e32dab1d026bc0f9c8ba00f8d42 | Python | 7,141 | 190 | #!/usr/bin/env python3
# Copyright 2020 - 2021 MONAI Consortium
# 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... |
520981349aa27974fb286c6d643301402388a98b26639b64c4bd1e90524fb4e8 | Python | 7,146 | 183 | from dataclasses import dataclass
from typing import Dict, Tuple
import scipy
from jax import numpy as jnp
from deeperwin.configuration import Configuration, PhysicalConfig, DistortionConfig
from deeperwin.loggers import LoggerCollection, WavefunctionLogger
from deeperwin.mcmc import MCMCState
from deeperwin.run_tools.... |
2fa68c16ae9a2266e6a6d83cf615facea7795a91748e349804ece13a707e3680 | Python | 7,148 | 266 | from __future__ import annotations
import functools as ft
import importlib.resources
import json
import re
from typing import Any, Callable, Dict, Iterable, TypeVar
import attrs
import more_itertools as itx
from typing_extensions import Protocol
from snakebids.utils.sb_typing import UserProperty
T = TypeVar("T")
... |
96a83f8bbb21058c1dd80ab704ae647116fc7322e971e23513e4eeb54e600d32 | Python | 7,148 | 173 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Federated averaging with secure aggregation module."""
import numpy as np
from openfl.interface.aggregation_functions.weighted_average import WeightedAverage
from openfl.utilities import LocalTensor
class SecureWeightedAverage(Weight... |
a94d67063a4dc575263c9db1c6bf2452662829fce3242c81f9b0f86e50f29e83 | Python | 7,148 | 173 | import os
import tables
import numpy as np
import nibabel as nib
import shutil
from tqdm import tqdm
from glob import glob
from config_trans import cfg
# Input shape: 240x240x155
def read_brain(brain_dir, mode='train', x0=29, x1=221, y0=29, y1=221, z0=2, z1=146):
"""
A function that reads and c... |
abb14d8063043e8ebf59810bab411296fd8ba340576a6ad5c723f91838327c8c | Python | 7,149 | 225 | """
Created on Sat September 16 21:15:06 2023
Description: Additional utilities functions for
Paper url: https://www.biorxiv.org/content/10.1101/2023.09.11.557230v2
@author: Ekaterina Kuzmina, ekaterina.kuzmina@skoltech.ru
@author: Dmitrii Kriukov, dmitrii.kriukov@skoltech.ru
"""
import numpy as np
from sklearn.deco... |
8ebeb3cb5095db15b184c71880d019b870a9590aa869df45fa579ab8447ed4a9 | Python | 7,154 | 210 | # -*- 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,... |
94351f6d3330e5be6402a3f1d210899adcf2db6af279019a20992ee40f4f03c5 | Python | 7,154 | 182 | """Tests for timeseries permutation tests and helper functions."""
import pytest
import numpy as np
from nltools.algorithms import circle_shift, phase_randomize
class TestCircleShift:
"""Tests for circle_shift() function."""
def test_random_shift_never_identity_1d(self):
"""A random 1D shift must n... |
f454d5fb38412b8626ce75a280ddb97e5e1e3beaa693c89925f40f39c9f58c7d | Python | 7,157 | 191 |
import string
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.oc... |
26581cf662994807b9c2299d69b3ba3c4c324b0da16bd2e18b94712670e6de6b | Python | 7,159 | 213 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import sys
from openfl.experimental.workflow.interface import FLSpec, Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from openfl.experimental.workflow.placement import aggregator, collaborator
cl... |
68044778d1aefb888f772bda8c2a6032246601df8bb122e30eb11bda6e01e31a | Python | 7,162 | 199 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates 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 Cogn... |
9fa56641faa43b1a3309502ac0f595f0cb3495862d577a363a4701edd84cd19a | Python | 7,163 | 155 | """
Differential Evolution
======================
In this tutorial, you will learn how to optimize PyRates models via the
`differential evolution <https://en.wikipedia.org/wiki/Differential_evolution>`_ strategy introduced in [1]_.
It will be based on the same model and the same parameter as the single parameter grid ... |
1d360bb94c34bd5cf95262d7fc90b68fe80d5b58fae75ccb9e3d5550dbf0c515 | Python | 7,166 | 157 | from DeepPurpose import utils, dataset
from sklearn.model_selection import train_test_split
from DeepPurpose.utils import *
import itertools
import torch
import numpy as np
from AutoEncoder import AutoEncoder
from torch.utils.data import DataLoader, Dataset
from torch import nn
import random
import wandb
from tqdm impo... |
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