sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
67e89db3cc019b7bf9f9b78997468b569e79c5ae8f7c0abea361a389c7e0ec35 | Python | 21,470 | 497 | # -*- coding: utf-8 -*-
import numpy as np
from sklearn.decomposition import PCA
from sklearn.manifold import Isomap
from sklearn.manifold import SpectralEmbedding
import functions.time_functions as tf
import copy
from scipy.linalg import svd
import functions.prediction
from scipy import stats
from typin... |
189516d399d83527920e202bc0153f44c8f46d23b1053fa5794028c433620fd6 | Python | 21,471 | 627 | import os
import numpy as np
from seriate import seriate
import gzip
from scipy.spatial.distance import pdist
from calc_stats_ms import N_ton, distance_vector, min_dist_ref, s_star_ind, num_private, label
from seriate import seriate
from scipy.spatial.distance import pdist, cdist
from scipy.optimize import linear_su... |
31fc7fc8f0f958bda0184895b6f077493ffc5cca006d37b9c2c0b3398554152d | Python | 21,481 | 593 | """Functions and classes for data preprocessing
Provides functions to turn multiple alignments from fasta files
into 'neural-network-readable' representations that can be
transformed into tensor datasets using
the child classes of *torch.utils.data.Dataset*
"""
import errno
import os
import warnings
import psutil
imp... |
9da4939c3a241c9f7f88f355b407f591f5c7b5679d2c798d89c8c9dc8b18b973 | Python | 21,541 | 535 | """Glass-brain, slice, flatmap, timeseries, and histogram plots for `BrainData`."""
import os
import warnings
import numpy as np
from nltools.utils import _find_stack_level
from .utils import _result_from_array
DEFAULT_SLICE_CUT_COORDS = {
"x": list(range(-50, 51, 8)),
"y": list(range(-80, 50, 10)),
"z... |
b7e98f502910423a029c6cb6fb4b0ebee82b03ae9f7a3fe5c7828656280158f5 | Python | 21,634 | 572 | """Export one loaded SanPy ``bAnalysis`` current-clamp recording to NWB.
This is a standalone development script. Edit ``ABF_PATH``,
and ``NWB_PATH`` in the ``__main__`` block before running it.
run with:
uv run --with pynwb scripts/nwb/export_sanpy_banalysis_to_nwb.py
"""
from __future__ import annotations
im... |
dc6b358ce830a7452ef287b1f5ad8791620a894f1c0e8adc2b97748dff9062f1 | Python | 21,643 | 648 | """Riemannian and pseudo-Riemannian metrics.
Lead author: Nina Miolane.
"""
from abc import ABC
import joblib
import geomstats.backend as gs
import geomstats.geometry as geometry
from geomstats.geometry.connection import Connection
from geomstats.vectorization import check_is_batch
EPSILON = 1e-4
class Riemannia... |
421df4904e9cb36051cd129214592e3b7e201b1fbfc36481145468e33b81266b | Python | 21,646 | 616 | #!/usr/bin/env python
'''
Keisuke Suzuki <ksk@chain.hokudai.ac.jp>
2023-01-27
'''
import os
os.environ['GLOG_minloglevel'] = '2' # suprress Caffe verbose prints
import settings
import site
site.addsitedir(settings.caffe_root)
import caffe
import numpy as np
import math, random
import sys, subprocess
from IPython.dis... |
2cc0d55e60613f5a56a0f6a6e80adab3fe00970fbdeb31ae3c73c17ef2a8ae92 | Python | 21,684 | 498 | import torch
import numpy
import pickle
import datetime
import pytorch_lightning as pl
from os.path import exists
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
import pandas as pd
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import torch.nn as nn
import torch.nn.fu... |
f3570ee67c012a5a42da48d5d28585993c055a192bef41eae599a5b52af45067 | Python | 21,715 | 514 | import os
import time
import pickle
from utils import *
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
# caution: Kekule form (no aromatic bonds), lower case, what about [cs], ccs?
# length of 2 only
Elements_2 = ['He', 'Li', 'Be', 'Ne', 'Na', 'Mg', 'Al',
'Si', 'Cl', 'Ar', 'Ca', 'Sc', 'Ti', '... |
f15dd174fb10df0ec1562e21d9c5f0c1d54d8c110021f8be86c65f9babcafdb4 | Python | 21,732 | 464 | """
Visual feedback with online decoding
Kyuhwa Lee
Swiss Federal Institute of Technology Lausanne (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 you... |
5d1da5c57686c6db1ad1e8c144bdd9caec268244141a6aa8dc97979467fff921 | Python | 21,789 | 711 | from PyQt5.QtWidgets import QApplication, QLabel, QGridLayout, \
QSizePolicy, QWidget, QPushButton, QFileDialog, QLineEdit, QDialog, \
QProgressBar, QMessageBox, QCheckBox, QListWidget, QTreeWidgetItem, QTreeWidget
from PyQt5.QtGui import QPainter, QKeyEvent, QDoubleValidator, QIntValidator
from PyQt5.QtCore im... |
dde9730309f28e941ee41cba3a0ea15c9312b9d25f4f34e41b50e2ecbc8a4fe8 | Python | 21,804 | 372 | import sys
import numpy as np
from scipy import sparse
from scipy.io import savemat, loadmat
import time
import multiprocessing as mp
from suns.Online.functions_online import merge_2
from suns.PostProcessing.seperate_neurons import watershed_neurons, separate_neuron
from suns.PostProcessing.combine import unique_neuro... |
85dc3b5b84f8dc6a17fab7f7ca3e155648b5097808630a11ca8b43f355eb2e48 | Python | 21,879 | 427 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this sof... |
11a607533679eed7fc92bba278794e111af19e7ade7d8e1ffd01908f85ea3661 | Python | 21,891 | 365 | import os
import sys
import numpy as np
import NALSM_GEN_SUPPORT as sup
import spatial_network_builder_lib as snb
class build_networks:
def __init__(self):
self.main_Path = os.getcwd()
self.codePath = self.main_Path
self.dataPath = self.main_Path + '/networks'
np.ra... |
c87b652a005b537484003e1fdf58d37444ccf4139c3492c3ed331e7fef2f1732 | Python | 21,910 | 597 | import numpy as np
from utils import *
import torch.nn as nn
import torch
import wandb
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from scipy.cluster.vq import kmeans2
from joblib import Parallel, delayed
def get_evs_stim_bifurc(Ks, evs):
"""
Sort the eigenvalues fo... |
3aedee889f23a0892f6332036d2df3a556baacc338bb8cdb5c759d57d1535914 | Python | 21,912 | 451 | # Copyright (C) 2022-2024 TU Darmstadt
# SPDX-License-Identifier: Apache-2.0
# -----------------------------------------------------------
# Primary author: Phillip Rieger <phillip.rieger@trust.tu-darmstadt.de>
# Co-authored-by: Torsten Krauss <torsten.krauss@uni-wuerzburg.de>
# ---------------------------------------... |
6a6b1b5e13f008be983cf986527172d019b5a96f7fbb96025c2719e624fc7d34 | Python | 21,949 | 539 | from __future__ import absolute_import
import warnings
import numpy as np
import pandas as pd
import os
import copy
from sklearn.preprocessing import StandardScaler
from pysurvival import utils
from pysurvival.models import BaseModel
from pysurvival.models._survival_forest import _SurvivalForestModel
from pysurvival im... |
7b526c72afb59f4311ff4a5479e3230a2a68b062c596302b533949842946cb2e | Python | 21,950 | 378 | # %%
import sys
import os
import random
import time
import glob
import numpy as np
import h5py
from scipy.io import savemat, loadmat
import multiprocessing as mp
import tensorflow as tf
import gc
os.environ['KERAS_BACKEND'] = 'tensorflow'
# os.environ['CUDA_VISIBLE_DEVICES'] = '0' # Set which GPU to use. '-1' uses onl... |
5264a5f3528745c577aa6f0b9578f9268d339ccd916c97eea6df04b90478e656 | Python | 21,965 | 478 | import tensorflow as tf
import variational.activations as variational_activations
class VariationalLayer(tf.keras.layers.Layer):
def __init__(self,
# weight_prior,
variance_parameterisation_type,
activation=None,
use_bias=True,
... |
39680d1be51ec4bc02d1b0fd7304cacf36c1817def7c138b507af14b154b5ead | Python | 21,993 | 607 | # 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 app... |
3a461707af034db6aeb87891fc80c0f911c75171e288fbae73f204ca3293882a | Python | 22,001 | 500 | # 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... |
10124987854594587a5662373b96495c45b49b46f8c9c2b27d8c1b7be002706b | Python | 22,024 | 567 | import math
import pytest
import geomstats.backend as gs
from geomstats.geometry.spd_matrices import SPDMatrices
from geomstats.test_cases.geometry.connection import (
ConnectionComparisonTestCase,
ConnectionTestCase,
)
from geomstats.test_cases.geometry.mixins import DistTestCaseMixins
from geomstats.vectori... |
f84209559faaa2404100dbc73c50ea0af65a4f431f2c073ee4331b13c3815c96 | Python | 22,025 | 532 | # Copyright (c) 2022 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... |
ae3d3672288bd24be023051c426ab84abd552da245aa538e8ea949050b06b214 | Python | 22,047 | 596 | from __future__ import absolute_import
import torch
import numpy as np
import copy
import multiprocessing
from pysurvival import HAS_GPU
from pysurvival import utils
from pysurvival.utils import neural_networks as nn
from pysurvival.utils import optimization as opt
from pysurvival.models import BaseModel
# %matplotli... |
7ef76b8f2c7ad2456f7b1682c82ebbc6eb3ab0bd999ea1ff1b6ce1fca02610f4 | Python | 22,053 | 527 | import argparse
import json
import os
import sys
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from pydfc import data_loader
from pydfc.data_loader import find_subj_list
from pydfc.ml_utils import find_available_subjects, load_task_data
from pydfc.task_utils import (
... |
bd5cd86ede8fa26dd9c23bfb535a5fbd553a7b3af73f7172a4bed99392cfad3d | Python | 22,081 | 655 | import itertools
import math
import geomstats.backend as gs
from geomstats.geometry.special_orthogonal import SpecialOrthogonal
from geomstats.test.data import TestData
from .base import LevelSetTestData
from .lie_group import LieGroupTestData, MatrixLieGroupTestData
from .mixins import ProjectionMixinsTestData
def... |
b12c4e79ae7e24656ecd6e052bcdbaeecb293aa3b5251725948ee8cfc6ea067b | Python | 22,087 | 638 | from __future__ import absolute_import
import numpy as np
from numpy.testing import assert_allclose
from nose.tools import assert_equal, assert_true, assert_raises, raises
import pycircstat
axis_1arg_test_funcs = [pycircstat.astd,
pycircstat.avar,
pycircstat.mean,
... |
7ad05ae3da058ce17a8204c9b4522ce5047cf4896e99008a2acf034a15048bf1 | Python | 22,108 | 378 | # %%
import sys
import os
import random
import time
import glob
import numpy as np
import h5py
from scipy.io import savemat, loadmat
import multiprocessing as mp
import tensorflow as tf
import gc
os.environ['KERAS_BACKEND'] = 'tensorflow'
# os.environ['CUDA_VISIBLE_DEVICES'] = '0' # Set which GPU to use. '-1' uses onl... |
81ee80a878305ca8d18bc5f5e9d4531664dc6d2ada36bcf4b6a15f071dacfcb0 | Python | 22,114 | 510 | """
This program trains a CNN on image patches from a stem cell microscopy dataset with 4 classes.
CNN's are trained with and without the addition of generated image patches
"""
from __future__ import division
import torch
import torch.nn as nn
import torchvision.transforms as transforms
import torch.utils.data.sampl... |
3d5c22e99a107adc90017210d1abbe379a9034878b16afd569b80e4312694064 | Python | 22,116 | 602 | """Permutation tests and dependence measures for square matrices.
`matrix_permutation_test` is the Mantel test: it asks whether two square matrices
(e.g. two representational dissimilarity matrices, or a brain and a model
similarity matrix) are correlated, building the null by permuting the rows and
columns of one mat... |
7f44b7c265b341ae803ae18c36f22988d911d2cc571604a46e7188a2448d7ddf | Python | 22,124 | 749 | import unittest
import torch
import torch.utils.data as tud
from reinvent.models.transformer.core.dataset.paired_dataset import PairedDataset
from reinvent.models.transformer.core.vocabulary import SMILESTokenizer
from tests.models.unit_tests.libinvent.transformer.fixtures import mocked_vocabulary
from tests.test_dat... |
14988b3c33f7b3c7ab29bb99a8da60ac41e8c0913cd06a35cf82cc663b0bc83e | Python | 22,168 | 487 | """Test suite for basic backend simulation functionalities.
"""
# external _imports
from typing import Union
import numpy as np
import pytest
# pyrates internal _imports
from pyrates import integrate
# meta infos
__author__ = "Richard Gast, Daniel Rose"
__status__ = "Development"
###########
# Utility #
###########... |
ccc2849b77c08934e6bbf3d12a18018bd865a91e10b9f20c6a3788d48c22d670 | Python | 22,198 | 555 | from typing import List, Literal, Optional, Tuple
import torch
from torch import nn
from .._weights import download_weights
from ..modules import Conv2dBlock, Conv3dBlock, UNetAttentionConv, _get_padding
def _flatten_z_to_channels(x):
return x.permute(0, 4, 1, 2, 3).reshape(x.size(0), -1, x.size(2), x.size(3))
... |
dd2a1358003a985b815b56bf262a7356871af60f56bd3f5b10ff26f98ddf773a | Python | 22,208 | 432 | """The dashboard's panels, in matplotlib.
Five of the dashboard's eight figures are ordinary geoms. They are drawn here instead of in R, in
the style the VDJdb papers already use: `~/vcs/manuscripts/2026-vdjdb-update` has no R at all --
every published figure is matplotlib with an Arial 7pt / 0.6pt-linewidth rcParams ... |
6def0646c7870859436257ad79eaed61e0d2f318ce76ed2da35ed6eb84dda89b | Python | 22,224 | 613 | """Embed the NicePool linked-plot component in a SanPy plugin."""
from __future__ import annotations
from collections.abc import Mapping, Sequence
from typing import Any
import pandas as pd
from PyQt5 import QtWidgets
import sanpy
from sanpy.bAnalysisResults import get_plot_result_definitions
from sanpy.interface.p... |
87ef781ae5b15b539a6068aa4bda81f0b128ff858597c517bf0191882dc33f6c | Python | 22,252 | 605 | """Provide standalone statistical functions for Adjacency matrices.
Each function takes an Adjacency instance as its first argument (`adj`).
"""
import numpy as np
def _similarity(
adj,
data,
plot=False,
method="2d",
n_permute=5000,
metric="spearman",
include_diag=False,
nan_policy="... |
cd06d0bd6a7f55b932dcbb8788d2792b307ae754a361f7bb738fa2d90f5a8dcc | Python | 22,257 | 499 | # -*- coding: utf-8 -*-
"""
This script resimulates observation data from the ground truth of the
`LoDoPaB-CT dataset <https://doi.org/10.5281/zenodo.3384092>`_ with a different
setting:
* A fan beam (2d cone beam) geometry is used instead of 2d parallel beam.
* 5% Gaussian noise is added to the post-log obser... |
d5050b41ed467e59c718e935a9d8aedac2c8a20d5023aaa8184f77956d226b37 | Python | 22,263 | 503 | import io
import json
import click
import pandas as pd
from uniprotparser.betaparser import UniprotParser, UniprotSequence
from sequal.sequence import Sequence
from curtainutils.common import read_fasta
def lambda_function_for_diann_ptm_single_site(
row: pd.Series,
modified_seq_col: str,
e... |
1d31ce3434e7a0f986f960f2cd7ac4b0dbb49c489dc4d8695c5cc2dc7b7e2c4b | Python | 22,290 | 634 | # in this script to fellow fairly closely Zou et al
# but the create a equivariant descriptor for each type
# of tree topology from the beggining
# We use a an embedding "across sequences" instead to
# within sequences.
# this is an optimized version of the lstm network
import numpy as np
np.random.seed(1234567)
# ... |
33ec2863f2bb6846c3457778c50a56f0e514d08b0bddb15e157360d93fd1bbf9 | Python | 22,322 | 551 | import argparse
import ast
import dataclasses
import logging
import os
import urllib.request
from copy import deepcopy
from typing import Any, Dict, List, Optional, Union
import torch
from mace.cli.fine_tuning_select import (
FilteringType,
SelectionSettings,
SubselectType,
select_samples,
)
from mace... |
8e107f6c10b9c9e7112ecdbecd529c32bdf5a4ff53dc0fdbcc89dc30d3497058 | Python | 22,389 | 395 | """Junctions that contradict the germline anchors of the V and J they name.
VDJdb's ``cdr3`` is junction space: Cys104 through Phe/Trp118, **both anchors included**. A
submission in IMGT CDR3 space, one carrying framework past an anchor, or one with a mis-read anchor
residue is none of those, and it passes every rule ... |
592dd42c546cfe749709a2a03c1bb2d42e72ff203d2ddb7449e42b60914f0881 | Python | 22,401 | 665 | # 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... |
043fb08c14696e38260c965fbf0eb7c028fc43b1b334ebfbdc1d19864d760bbb | Python | 22,501 | 537 | """Classes for fiber bundles and quotient metrics.
Lead author: Nicolas Guigui.
"""
import geomstats.backend as gs
from geomstats.geometry.riemannian_metric import RiemannianMetric
class QuotientMetric(RiemannianMetric):
"""Quotient metric.
Given a (principal) fiber bundle, or more generally a manifold wit... |
bdfc2ab37ddfc06bc22928facb1d597fdf7ad54b305a84ab27800045a54b1202 | Python | 22,501 | 536 | # Copyright (c) 2023 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... |
e57b783a402a41d25ebb1325a3807d1b22297bc084cb91e2ef2f2853ab78a90c | Python | 22,513 | 642 | ### COMMAND FORMATS
__description__ = \
"""
PyCmdMessenger
Class for communication with an arduino using the CmdMessenger serial
communication library.
"""
__author__ = "Michael J. Harms"
__date__ = "2016-05-20"
import serial
import re, warnings, multiprocessing, time, struct
class CmdMessenger:
"""
Basic... |
dbb71ade319fadd43b8d9da5121facf519e8144125d0713ef60fc46f69e6bc1d | Python | 22,566 | 597 | """Unit tests for mace/tools/multihead_tools.py.
Covers the pure/offline pieces: HeadConfig construction and defaults,
dict_head_to_dataclass (head-dict overrides vs. args fallbacks + the
missing-train_file error), prepare_default_head with the real arg parser,
and both branches of prepare_pt_head (neither branch down... |
d83ee2f75811f96ad9a681838b8065430f59360282cd3ad230fa3c3c16a8fd2a | Python | 22,585 | 635 | """Generate m sequences.
Loosely translated from http://fmriserver.ucsd.edu/ttliu
"""
from __future__ import annotations
import math
import numpy as np
from rich import print
class Msequence:
"""Create instance for an order of experimental trials."""
def __init__(self):
# read in taps file and co... |
f7f3e08a0119404efcd675f174c0634a192605700f5f34d811be40372a3690ed | Python | 22,586 | 544 | import warnings
import numpy as np
import nibabel as nib
import pytest
from nltools.data import BrainData
from nltools.templates import get_brainspace
class TestBrainDataInit:
"""Test BrainData initialization, resampling, and template auto-detection."""
def test_init_resample_true_mismatched_spaces(self):
... |
c1c6f5470c411b3eb096ece74eb722f96498a96f59aa4914e056ea3cf4a8975e | Python | 22,609 | 569 | from typing import TYPE_CHECKING, Optional, Union, List, cast
from chromadb.api.types import (
URI,
CollectionMetadata,
Embedding,
PyEmbedding,
Include,
IndexingStatus,
Metadata,
Document,
Image,
Where,
IDs,
GetResult,
QueryResult,
ID,
OneOrMany,
ReadLeve... |
f77cff339ecb49d71baae3e47c2296c95fb45deb03deb24b8e4c0c1225935574 | Python | 22,633 | 579 | """
ResNet code gently borrowed from
https://github.com/pytorch/vision/blob/master/torchvision/models/resnet.py
"""
from __future__ import print_function, division, absolute_import
from collections import OrderedDict
import math
import torch.nn as nn
from torch.utils import model_zoo
__all__ = ['SENet', 'senet154', 's... |
a5a248d355d92d193c259e28c69d66f1bb57e684625c1c320a9ad9b792cb701b | Python | 22,641 | 437 | """
File containing the wavefunction model & function to build the model
"""
import haiku.experimental
import jax
import jax.numpy as jnp
from typing import Optional, Dict, Callable, Any, Tuple, Union, List
import haiku as hk
import logging
from deeperwin.configuration import (
ModelConfig,
JastrowConfig,
... |
575bb6103696ac9fc902e3f822739d7b80d7bde28347c27483af108a78f3589b | Python | 22,647 | 601 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon May 1 15:05:23 2023
@author: shah
"""
from tensorflow.keras.layers import Dense, Layer
import tensorflow as tf
import numpy as np
import collections
from tensorflow.keras import Model
from tensorflow.keras.layers import (
Dropout,
Softmax,
... |
00cd9b4ee69abe67b67d704fc0ba2058bf0f78404a414866093244940c27ddd5 | Python | 22,674 | 458 | """IMGT segment nomenclature (#389): mechanical respellings only, never a guess."""
from __future__ import annotations
import polars as pl
import pytest
from vdjdb.curate import nomenclature as N
@pytest.mark.parametrize("call,expected", [
# the /DV genes IMGT names once for both loci -- 1,377 chains write the ... |
863fc5f489824126711145fcc4c7f53244aafa47b23787bf585641ff24fa6b2d | Python | 22,689 | 631 | import click
import os
import math
from corgie.block import get_blocks
from copy import deepcopy
from corgie import exceptions, stack, helpers, scheduling, argparsers
from corgie.log import logger as corgie_logger
from corgie.layers import get_layer_types, DEFAULT_LAYER_TYPE, str_to_layer_type
from corgie.boundingcub... |
f36b0a9d016979ae4fdc6ae4168043fa9b60b78038483fefb802d3dd318cc2f0 | Python | 22,719 | 447 | import numpy as np
# import tensorflow as tf
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import os
import sys
import time
import NALSM_CONSTRUCTOR_MNIST as construct
import NALSM_PARALLEL_SAVE as parasaver
import NALSM_SIM_SUPPORT as runSupport # NEW PARALLEL FILE
import NALSM_GEN_SUPPORT as su... |
9c44727d93d02a985aaba2c7f0854e3081dc2ae64a08241222194799cb44877e | Python | 22,734 | 645 | import torch
import torch.nn as nn
import numpy as np
import os
import sys
file_dir = os.path.dirname(__file__)
sys.path.append(file_dir)
from initializers import *
class RNNCell(nn.Module):
def __init__(self, params):
"""
Full rank RNN cell
Args:
params: dictionary with model... |
53c7d79e846cabc53c8ccde3673d1901abf52b94b21f844ab9b99bb05aa26342 | Python | 22,756 | 713 | import httpx
from typing import Optional, Sequence
from uuid import UUID
from overrides import override
from chromadb.auth import UserIdentity
from chromadb.auth.utils import maybe_set_tenant_and_database
from chromadb.api import AsyncAdminAPI, AsyncClientAPI, AsyncServerAPI
from chromadb.api.collection_configuration ... |
190235a0ec0611a0427f7198dee329b2db49317b4f2b771d9bd88e693838821a | Python | 22,758 | 632 | # 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... |
57c7ed9c5794c09c6ea016a177908e1fc951c57fe6e267528edabc26397a9f72 | Python | 22,773 | 478 | #!/usr/bin/env python3
# Script parse sniffles2 vcf files and extract useful information
# USAGE: cat sv_file.vcf | python3 sniffles2_vcf_parser.py
# important imports
import sys
import argparse
import random
# Version
def the_version():
print(f'sniffles2_vcf_parser.py\nversion 0.1')
# log output
def logger(... |
826c6f5ec4184de943424de206468d7ebced584c0d63c3bd4efcbfbc904348c2 | Python | 22,838 | 574 | import copy
import torch
import numpy as np
import torch.nn as nn
from tqdm import trange
from sklearn.model_selection import StratifiedKFold
from torch_geometric.loader import DataLoader
from sklearn.svm import SVC
from sklearn import preprocessing
from sklearn.metrics import accuracy_score
from sklearn.model_selecti... |
6c1271803b6359deec65007646ef2768b483437df3623d670c43dba315cf7656 | Python | 22,864 | 547 | """Module that implements the CWT using a trainable complex morlet wavelet"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
from sleeprnn.data.utils import get_kernel
def compute_cwt(
inputs,
fb_list,... |
a886f827e10c40d1960fd48212d21717120b5b59bafac8a237c9c8dc8490f095 | Python | 22,871 | 605 | """Main user interface for FISSA.
Authors:
- Sander W Keemink (swkeemink@scimail.eu)
- Scott C Lowe
"""
from __future__ import print_function
from past.builtins import basestring
import collections
import glob
import os.path
import sys
import warnings
import numpy as np
from scipy.io import savemat
from . ... |
c428d20424cd181c2beb3d3c9d3ae78372b739c45fd746f9a9f2d184a0d68de7 | Python | 22,902 | 559 | import os
import shutil
from overrides import override
import pickle
from typing import Dict, List, Optional, Sequence, Set, cast
from chromadb.config import System
from chromadb.db.base import ParameterValue, get_sql
from chromadb.db.impl.sqlite import SqliteDB
from chromadb.segment.impl.vector.batch import Batch
from... |
eaa2350761aff19b443285697120c5091457fe39a1f729305efda301043319d9 | Python | 22,904 | 489 | """
FES feedback with online decoding
Kyuhwa Lee
Swiss Federal Institute of Technology Lausanne (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 o... |
4b9f5e76d6e717a6041665d78368b97039d7c101e43a353bd6c325cdff1586ea | Python | 22,913 | 534 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
7b1f281557364dfcc09639ee869c26c7acbfda6ddabade3297616bcf6052c5c6 | Python | 22,924 | 609 | # -*- coding: utf-8 -*-
# OS stuff
import os
import sys
import warnings
from pathlib import Path
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib import font_manager as fm
from matplotli... |
13c7b43b066f91904ad3c19008ed11f0e909278e8a973619d0feb678f520d1ec | Python | 22,939 | 543 | """General linear model estimator built on Nilearn's `run_glm`.
`_Glm` fits one run represented by a `(DesignMatrix, y)` pair. It knows nothing
about `BrainData`, masks, NIfTI images, events, or multi-run orchestration: the
caller supplies a precomputed design (including any intercept column) and a
preprocessed respon... |
598af276189c478cff0c6aa0cb87db1275bb9f82c3fd7d52ef18557c4c64ecae | Python | 22,946 | 557 | # Copyright (c) 2023 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... |
7d6960f721754e8ac52c2a9eb69f289d17cd2ef6a272e7e1b211223cc6e82413 | Python | 22,950 | 655 | """
Label Object
and functions dealing with labels
"""
import copy
import numpy as np
from typing import List, Tuple, Union
from scipy.sparse import csr_matrix, issparse
from scipy.optimize import linear_sum_assignment
import matplotlib as mpl
from mpl_toolkits.axes_grid1 import make_axes_locatable
f... |
846b0e47093d8cd78436a6bd9a0bea970cc9d3c359d28477f5530fa9a7457fab | Python | 22,950 | 623 | # 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... |
f59c772ec902bdf803779ab833444988e3d29084e33a76d74744f09f33654cb9 | Python | 23,000 | 583 | """Module that defines as base model class to manage neural networks."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import json
import os
import numpy as np
import tensorflow as tf
from sleeprnn.common import pkeys
from sleeprnn.common import constan... |
f1d4e8d43db99b912a73bbfacddff6c6680c23a0cf87d718a31d8739babd7882 | Python | 23,001 | 562 | import json
import os
import cv2
import ffmpeg
import numpy as np
import pandas as pd
import torch
from scipy import signal
from scipy.spatial.transform import Rotation as R
from sklearn.metrics import f1_score, recall_score
from torch.utils.data import DataLoader
from utils.hand.AD import cal_error_frame_ratio
from u... |
5cdbdb33fbcba2bc6732f469432fba52adf95013cad50523b8c135cab2e079d9 | Python | 23,003 | 579 | """Module that stores several useful keys to configure a model.
"""
from . import constants
""" Input pipeline params
batch_size: (int) Size of the mini batches used for training.
shuffle_buffer_size: (int) Size of the buffer to shuffle the data. If 0, no
shuffle is applied.
prefetch_buffer_size: (int) Size of ... |
3b8db1cf252c03236ec6226e41966dec7b460fd5a66d261e6c853a79123c6071 | Python | 23,009 | 614 | ###########################################################################################
# Data parsing utilities
# Authors: Ilyes Batatia, Gregor Simm and David Kovacs
# This program is distributed under the MIT License (see MIT.md)
###################################################################################... |
a8a3c5883866243a0fd2441f9eebf35dfb969b1bd625691cab7e4870bed91f40 | Python | 23,045 | 636 | from PymoNNto.Exploration.UI_Base import *
from PymoNNto.Exploration.StorageManager.StorageManager import *
from PymoNNto.Exploration.Evolution.SSH_Functions import *
from PymoNNto.Exploration.Evolution.EvolutionPlots import *
from multiprocessing import Process, Queue, Pipe
import shutil
import os
class QHLine(QFrame... |
96faa832bafe5ef9dda3bb29905b5fdd7b175ec5b9073a43a98482aae12fff42 | Python | 23,057 | 668 | """Brain visualization — surface plots and flatmaps."""
import os
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from nilearn.plotting import plot_surf_stat_map
from nilearn.surface import vol_to_surf
def _resolve_stat_map_defaults(data, *, cmap=None, vmin=None, vmax=None):
"""Resol... |
30b8c6ddeac4b1f9672dba81b568951d587152fecdcd3448ada77543922ae811 | Python | 23,091 | 282 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 18.10.2021
# Author: Moritz Smolka
# Contact: moritz.g.smolka@gmail.com
#
import os
import sys
import datetime
import argparse
from sniffles import util
VERSION="Sniffles2"
BUILD="2.2"
SNF_VERSION="S2_... |
3c447f2cb20596614e51cd4ac8b90964e90264d407063edb0d4642037380ce32 | Python | 23,097 | 615 | import pytest
import geomstats.backend as gs
from geomstats.geometry.special_orthogonal import (
SpecialOrthogonal,
_SpecialOrthogonal2Vectors,
_SpecialOrthogonal3Vectors,
)
from geomstats.test.random import (
LieGroupVectorRandomDataGenerator,
get_random_quaternion,
)
from geomstats.test.vectoriza... |
d0fe7e0363453c439dbcb514bd0d30d5912173dc5547cbeea0495aa767f202c0 | Python | 23,110 | 568 | # -*- coding: utf-8 -*-
# OS stuff
import os
import sys
import warnings
from pathlib import Path
from tqdm import tqdm
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpecFromSubplotSpec
from matplotlib import ticker
import matplot... |
716f5972f07dd1c461572c73cb147a1a1cb517615ddc2cc0448bb4ee7fc04ed5 | Python | 23,124 | 606 | #!/usr/bin/env python3
from ast import literal_eval
from typing import List, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from fairseq import checkpoint_utils, utils
from fairseq.data.data_utils import lengths_to_padding_mask
from fairseq.models import (
FairseqEncoder,
FairseqEnco... |
747edb74c448c6c89367802bcc8e337f7124f5bd7a9ef4265df77f3f197bfdb9 | Python | 23,140 | 501 | import os
import random
import logging as log
import coloredlogs
import cv2
import hydra
import numpy as np
import torch
import yaml
from common.itemloader import ItemLoader
from omegaconf import OmegaConf
from sklearn.metrics import roc_auc_score, balanced_accuracy_score, accuracy_score
from tqdm import tqdm
from ad... |
aa5b5b0de777988cb40cbb78578d142d07e24e9e6a1527a604a71fc74f098b10 | Python | 23,177 | 557 | import json
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from os import path
from os import mkdir
from csv import writer
from datetime import datetime
from sys import exit
class JSLog:
def __init__(self, experiment_name, sub_dir = None):
configuration_path = path.join(
... |
6533ff31e216381135c41bfbd71eacdbfe1c6cced81ad570e782c7599729a4be | Python | 23,199 | 700 | """Graph Space.
Lead author: Anna Calissano.
References
----------
.. [Calissano2020] Calissano, A., Feragen, A., Vantini, S.
“Graph Space: Geodesic Principal Components for a Population of
Network-valued Data.” Mox report 14, 2020.
https://mox.polimi.it/reports-and-theses/publication-results/?id=855.
""... |
0ff798db79b3eaf5e6fdc0977dfb90d58932a69b62abce5c7b12b37df7f3a81b | Python | 23,250 | 695 | """
Main BANKSY functions
Nigel 3 dec 2020
updated 4 mar 2022
updated 8 Sep 2022
"""
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import seaborn as sns
from typing import Union, Tuple, List
import scipy.sparse as sparse
from scipy.sparse import c... |
26b5703703b0db43ce06865e935e0e66bbf5ed72f2a333e7585503854bca3496 | Python | 23,279 | 402 | import io
import numpy as np
from scipy import sparse
from scipy import signal
from scipy.io import savemat, loadmat
import time
import multiprocessing as mp
from suns.PostProcessing.seperate_neurons import watershed_neurons, separate_neuron
from suns.PostProcessing.combine import segs_results, unique_neurons2_simp, g... |
8dec61b0ccb82862d5c6eee6e7567b0fda6b9c896f1bf91f9bb4511d2ce0a081 | Python | 23,311 | 673 | import numpy as np
import scipy.stats as stats
import pandas as pd
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
from umap import UMAP
from sklearn.covariance import MinCovDet
import matplotlib.pyplot as plt
import seaborn as sns
from shapely.geometry import Polygon
from itertools import co... |
ee7291df27c1cd0d76ae2b3d217da697725aae70ea63e04ab850d050331b8157 | Python | 23,315 | 379 | """Every motif metric, for three fixed sources, recorded and gated on every build.
The motif stage is the one place where the release cannot be reproduced byte for byte, so its
acceptance criterion is a set of measurements rather than a digest (``docs/clustering.md``). Those
measurements were being computed inside tes... |
1804e78642dc7ea8e24e6315c0d6ab444ed3b49cce25bfb06cde95439a48c2d1 | Python | 23,332 | 531 | ########################################################################################################################
# This script takes pairs of JSON files exported from EPPI reviewer using identical coding schemes on the same group of
# papers. Each JSON file includes annotations for a coder. The script produ... |
ed0d941d7b380c4986961af44b0340d6c163cd45d4fa53b16e5b77c5726c8da9 | Python | 23,342 | 498 | """The reference corpus: the MHC dictionary, the token families, the weighting, and the two queries.
The weighting is checked against ``sklearn.feature_extraction.text.TfidfVectorizer`` rather than only
against itself, which is the reason :mod:`vdjdb.corpus.build` uses that library's conventions: an
implementation agr... |
3aa4cd149cd012f067af500045b5c8c25b7479ad5b4fd6941df1c31142ea2b25 | Python | 23,355 | 569 | # -*- coding: utf-8 -*-
# OS stuff
import os
import sys
import warnings
from pathlib import Path
from tqdm import tqdm
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpecFromSubplotSpec
from matplotlib import ticker
import matplot... |
c661bdb92cec8cc90d262bb6ef6ae52a59f1f7f60b3440936bc5e4f9c2dc8d03 | Python | 23,417 | 554 | # 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... |
a05235e7315f738cf6335a503dcfe630b619824b322b7c4811a5c8fdd4cfda50 | Python | 23,447 | 678 | """
Streaming image data between processes
Author: Tal Eisenberg, 2021
The following classes use shared memory buffers to generate and process image data in an asynchronous manner using multiple os processes.
- ImageSource: a multiprocessing.Process that writes image data to a shared memory buffer.
- ImageObserver: a... |
469d74f3c66c77dfe19cea1dfc4a05ee4ce4d0aca169d987fbb406a6451e22d5 | Python | 23,473 | 485 | from __future__ import absolute_import
import numpy as np
import tensorflow as tf
import tensorflow.keras.backend as K
from color_ops import rgb2hsl_tf, rgb2yiq_tf
class NCC:
"""
Local (over window) normalized cross correlation loss.
"""
def __init__(self, win=None, eps=1e-5):
... |
d155cf3dca9540d8a7fe982a3cdb03a80ff1a47754f6aa8ab4645b6853f74b1c | Python | 23,510 | 560 | from PymoNNto.Exploration.Network_UI.Network_UI import *
from PymoNNto.Exploration.Network_UI.TabBase import *
def pol2cart(theta, rho):
x = rho * np.cos(theta)
y = rho * np.sin(theta)
return x, y
def cart2pol(x, y):
theta = np.arctan2(y, x)
rho = np.hypot(x, y)
return theta, rho
class DrawIt... |
60478f935f38285fed60da79c4b0581548da33eedad2b141e94c1cfd23d043bd | Python | 23,524 | 679 | """
Streaming image data between processes
Author: Tal Eisenberg, 2021
The following classes use shared memory buffers to generate and process image data in an asynchronous manner using multiple os processes.
- ImageSource: a multiprocessing.Process that writes image data to a shared memory buffer.
- ImageObserver: a... |
198eaca413e5708148698fe2d5166656045f6174a416291d566842b95aa4c31b | Python | 23,554 | 556 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import os
import shutil
import subprocess
from glob import glob
import logging
import importlib
from pathlib import Path
import json
import tests.end_to_end.utils.defaults as defaults
import tests.end_to_end.utils.exceptions as ex
from test... |
869a6ffaca02b477cbe0cf75c321ecf8dae355a48572091f549128751657b135 | Python | 23,555 | 571 | """Adding graph convolution encoding on top of the transformer encoder, utilizing `baseFunc.py` and `buildGraph.py`
for DGL graph construction, and implementing the split of graph convolution encoding within `transformer_layer.py`."""
import math
from typing import Dict, List, Optional
import torch
import torch.nn as... |
66fa82209bed776bf614f860940031a11005ff48bb9f44af3f06a2b43f2ddccc | Python | 23,576 | 612 | # 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... |
020104c08bf9dfc78a8a77b2497953a04ad1821f8c4ce72e3f33471cb650783d | Python | 23,579 | 708 | from Bio import SeqIO
from sgt import SGT
import pandas as pd
import os
os.environ['TF_CPP_MIN_LOG_LEVEL']='3'
import numpy as np
import tensorflow as tf
import sys
import time
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import argparse
# Create a parser
parser = argpars... |
92c819d5a7e865cff7c380f5a4157af801bf4491c3a25ba766120251f871b080 | Python | 23,587 | 642 | from chromadb.api.types import Embeddings, Documents, EmbeddingFunction, Space
from chromadb import __version__
from typing import List, Dict, Any, cast, Optional
import os
import numpy as np
import numpy.typing as npt
from chromadb.utils.embedding_functions.schemas import validate_config_schema
import warnings
class... |
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