sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e67ee78f76dd97f1d34f21767f37bcd4e900a1f6db2f5f1f0eb7efe2bb2e03fe | Python | 5,857 | 146 | import unittest
import numpy as np
from bsb import Configuration, ConfigurationError, Scaffold
from bsb_test import NumpyTestCase, RandomStorageFixture
class TestIoMolecular(
RandomStorageFixture,
NumpyTestCase,
unittest.TestCase,
engine_name="hdf5",
):
def setUp(self):
super().setUp()
... |
a75cfefa19d4bf44cc7b0c860aed969d2ebcd7176a84ea11c1e91011a14b44ed | Python | 5,859 | 178 | """
Plot Figure 3
"""
import numpy as np
import strinf as si
# # # PARAMETERS # # #
ZOOM = 1.5
SAVE = True
SHOW = True
PANEL = ("C", "E", "F") # The sketches in A, B, D are always plotted.
# data analysis obtained from '../ana/Yang_regress_and_choice.py'
fnameData = "./data/data_yang2021_experiment_1/yang_predic... |
5c82be5ebc7f6a8ba98904d597656ce7af916ee13412137c60a4e8419d4acbaf | Python | 5,862 | 145 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Obtain a TSNE projection of the reduced matrix
"""
import cellranger.analysis.pca as cr_pca
import cellranger.analysis.plsa as cr_plsa
import cellranger.analysis.lsa as cr_lsa
import cellranger.analysis.bhtsne as cr_tsne
import cellranger.analysis.io as a... |
5d90af5e0c015a339ad65742e54a0ca53d29718c122fa8c61214b779ddc4fbdf | Python | 5,864 | 145 | import os
import pytest
import tempfile
import numpy as np
import pandas as pd
import skimage.io as io
from ark import settings
from test_utils import make_cell_table
from alpineer import image_utils, test_utils, misc_utils
from ark.phenotyping import post_cluster_utils
def test_plot_hist_thresholds():
pops = n... |
8af1546ba0112e2a1a4ff3bc581ad0f5a954bcd67619b0832ecc559eda5be20a | Python | 5,866 | 143 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import numpy as np
import torch
from ax.generators.random.base import RandomGenerator
from ax.utils.co... |
729b9bbfe2dc2e1f622d4f708235503e06287822d6ce466c0943e1529a893dd0 | Python | 5,868 | 159 | """
Created on 2020.05.19
@author: Jiahua Rao, Weiming Li, Hui Yang, Jiancong Xie
Code based on:
Zheng, Shuangjia, et al. "Identifying structure–property relationships through SMILES syntax analysis with self-attention mechanism." Journal of chemical information and modeling 59.2 (2019): 914-923.
"""
import os, re... |
9590a164e403b5bb31e5867b2acc175a7cde392b5b00e387ab6facfe1669b543 | Python | 5,869 | 180 | """
Data providers that iterate over a source that is not in memory
or not in a file.
"""
import gzip
import logging
import subprocess
import tempfile
from urllib.parse import (
urlencode,
urlparse,
)
from urllib.request import urlopen
from galaxy.util import DEFAULT_SOCKET_TIMEOUT
from . import (
base,
... |
0a26140d883465d48b355fa044633f7d8e87933208ec456bd4bffd2762ee3270 | Python | 5,870 | 164 | import json
from pathlib import Path
from unittest.mock import patch
import nibabel as nib
import numpy as np
import pandas as pd
import pytest
from neurolang.frontend import NeurolangPDL
from neurolang_apps.utils import engine_registry
from neurolang_apps.utils.engines.neurostore import init as neurostore_init
NS_I... |
7bda4618e949030ff6fb0766196c7e26dd243ce8b518a3f9e148d9c200815740 | Python | 5,870 | 153 | import MDAnalysis as mda
import tqdm
import argparse
import jax
import jax.numpy as jnp
import pdb
import rlcompleter
pdb.Pdb.complete=rlcompleter.Completer(locals()).complete
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
parser = argparse.ArgumentParser()
parser.add_argument ('--topology',... |
f6f5a8845c1627b763b067ec9020f95274058b4e6aa31eb4b381ef9faa3713c3 | Python | 5,873 | 134 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
77c86cbfb96fff957e5f524e0dccc1801b68663194c8dfd38a8ee08e79d3ebbc | Python | 5,874 | 161 | # Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from ax.analysis.plotly.surface.slice import compute_slice_adhoc, SlicePlot
from ax.core.trial import Trial
from ax.exception... |
34e363a172a9f3b84b3aef6b22ce05b5e2a49f528189b0edd9a7dea2d3573d42 | Python | 5,877 | 131 | import pandas as pd
from sklearn.feature_extraction import FeatureHasher
import math
def init_directories(postprocess_folder):
if postprocess_folder == "all_products":
directory_g1 = r'../postprocess_all_products/g1'
directory_g2 = r'../postprocess_all_products/g2'
directory_g3 = r'../postp... |
af5179a95103667ccf9f9c89ef5469f99ee9ab7dc2cc915f6660e15417a447d6 | Python | 5,879 | 149 | import pytest
import networkx as nx
def validate_grid_path(r, c, s, t, p):
assert isinstance(p, list)
assert p[0] == s
assert p[-1] == t
s = ((s - 1) // c, (s - 1) % c)
t = ((t - 1) // c, (t - 1) % c)
assert len(p) == abs(t[0] - s[0]) + abs(t[1] - s[1]) + 1
p = [((u - 1) // c, (u - 1) % c... |
54fc280e6a2c0abde322af7700a295d4132b789b666c256d29fa28f5b8b7f210 | Python | 5,880 | 148 | """
Created on Jun 3, 2025.
@author: voodoocode
"""
import threadpoolctl
import os
import numpy as np
import matplotlib.pyplot as plt
import finnpy.file_io.data_manager as dm # @UnresolvedImport
import finnpy.src_rec.sen_cov # @UnresolvedImport
import finnpy.src_rec.coreg # @UnresolvedImport
import finnpy.src... |
114ee662572a3845a2b645797d5590531d5f435279b839a3efc0b4223880b7de | Python | 5,881 | 155 | import inspect
import logging
import os
import sys
import threading
import time
from multiprocessing.util import register_after_fork
from typing import (
Any,
Union,
)
from sqlalchemy import (
create_engine,
event,
exc,
)
from sqlalchemy.engine import Engine
from sqlalchemy.pool import NullPool
lo... |
978f50a53d950a9dc0391ef5d48db8362edde403a536863338599817d3c909e4 | Python | 5,882 | 149 | # -*- coding: utf-8 -*-
"""
Template to run the processing pipeline
"""
import os,numpy, sys
#pre-execute to make sure that Clearmap modules can be loaded
basedir = os.path.abspath(os.path.join(os.path.dirname(__file__),'../../..'))
sys.path.insert(0, basedir)
import ClearMap
#load the parameters:
parameter_filename... |
32ce14ef8ec79582a58b3277c8169e907c1a328575a062c6d00695fb2b10a087 | Python | 5,883 | 154 | #!/usr/bin/env python3
"""Kernel launch-parameter tuning harness for tsne-cuda.
The FFT-interpolation kernels expose their block sizes through GpuOptions, and
those can be overridden at runtime via environment variables (see
src/include/options.h):
TSNE_FFT_THREADS nbodyfft interpolation/copy kernels (defau... |
b5246cf5347bb3fe0cecc0ff6c5ef728060df306f4335df5e0861b0f3a07502c | Python | 5,883 | 189 | """
Contains all the mathematical helper functions used throughout the scaffold.
Differs from helpers.py only categorically. Helpers.py contains functions,
classes and general logic that supports the scaffold, while functions.py
contains a collection of mathematical functions.
"""
import bisect
import ... |
c46757360f0bd57c464a42ff06ad4bfe2e8f417c96bd5fe45c9e53da7e85636c | Python | 5,884 | 160 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from unittest.mock import MagicMock
from ax.exceptions.core impor... |
2b3f216fe0433f40a2c7f69d9ad5c9422ef683dae389f4229f6c0b43f9087fa6 | Python | 5,885 | 166 | """
#########################################################################################################
Author: Álvaro Fernández García
Date: 21 - Marzo - 2019
Description: Este script permite utilizar el clasificador GlandsDetector para
obtener una ayuda en el etiquetado de los datos. Permite clasificar una ima... |
2eeee731d62ed49555e7c7c4de1bfe77f6af4f2e61d323bd2ec23302df360a59 | Python | 5,885 | 202 | """Check a project and backend by attempting to build using PEP 517 hooks.
"""
import argparse
import logging
import os
from os.path import isfile, join as pjoin
from pip._vendor.pytoml import TomlError, load as toml_load
import shutil
from subprocess import CalledProcessError
import sys
import tarfile
from tempfile im... |
5a12fd78a1468b5f2fa2af3620a960abc2b317b7f5188f84a218a2bb9d721ef6 | Python | 5,885 | 211 | """test markers_combinator"""
import json
from pathlib import Path
import numpy as np
import numpy.testing as npt
from click.testing import CliRunner
from voxcell import VoxelData # type: ignore
import atlas_densities.app.combination as tested
TEST_PATH = Path(__file__).parent.parent
def test_combine_markers(tmp_... |
acd832e53dc736334785988eee4c7f532268cc2e29b06cfd352119ab1b66181a | Python | 5,885 | 184 | import os.path as osp
from itertools import product
import numpy as np
import scipy.io
import torch
import time
from cogdl.data import Graph, Dataset
from cogdl.utils import download_url
class MatlabMatrix(Dataset):
r"""networks from the http://leitang.net/code/social-dimension/data/ or http://snap.stanford.edu... |
558b871494d9b4e02b8b11dffb9c5e1fd2654830016528e345a909ad805c4564 | Python | 5,890 | 165 | """Structure-from-motion (SfM). Control experiment with additional motion components (= SI Figure)"""
import numpy as np
from datetime import datetime
from strinf import ObservationGeneratorVelo, WorldVeloFunction,\
FilterStrinfNaturalParameters, FilterStrinfAdiabaticDiagonalSigma,\
... |
81ada82d51502b12276d4032dc4a6e6b56b8bf39b4b0c287fc0c1241af238a5a | Python | 5,891 | 165 | # rmf 12.29.2020, last modified 5.13.2021
import sys, re
# INPUT: DAVID cluster motif summary file from hypergeometric testing
# OUTPUT: file with same information, filtered; additional columns for expression in young and old, and enrichment score
# FUNCTION: filters DAVID clusters by enrichment score and TFs by FPKM... |
22c8c302d62d51301564708979e2c84e04782c8a0350ae64c9024997d7262260 | Python | 5,896 | 216 | import numpy as np
from numcodecs import (BZ2, AsType, Blosc, Categorize, Delta, FixedScaleOffset,
PackBits, Quantize, Zlib)
from numpy.testing import assert_array_almost_equal, assert_array_equal
from zarr.creation import array
compressors = [
None,
Zlib(),
BZ2(),
Blosc(),
]
t... |
44ee7ad891042b907bab0632d66af79cda2a964b5d49549a20787fb574ecc66e | Python | 5,898 | 135 | from cogdl.utils import dropout_adj
import os.path as osp
import os
import argparse
import numpy as np
import torch
"""
The Following code is borrowed from SelfGNN
"""
class Augmentation:
def __init__(self, p_f1=0.2, p_f2=0.1, p_e1=0.2, p_e2=0.3):
"""
two simple graph augmentation functions ... |
cbe2950f2296c4f84383c32f03e044b6b4ff56e625f7c70befc1ec2ae635ac62 | Python | 5,898 | 152 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
f4d77d09f8829f6f74f0181167e71088c423a4e143bb805fb68775762756c821 | Python | 5,898 | 220 | import pytest
import networkx as nx
np = pytest.importorskip("numpy")
sp = pytest.importorskip("scipy")
def test_laplacian_centrality_null_graph():
G = nx.Graph()
with pytest.raises(nx.NetworkXPointlessConcept):
d = nx.laplacian_centrality(G, normalized=False)
def test_laplacian_centrality_single_... |
f14c8e7ff0bf5d910d0f0b32052b0d661f25f6a155c7387eefd4be8a73235862 | Python | 5,899 | 163 | import os.path as osp
import numpy as np
import scipy.io as sio
import torch
from cogdl.data import Graph, Dataset
from cogdl.utils import download_url, untar
def sample_mask(idx, length):
"""Create mask."""
mask = np.zeros(length)
mask[idx] = 1
return np.array(mask, dtype=np.bool)
class HANDataset... |
3e96bd1bd3db6c72625d7a2718f76b3fc31420a19ac916b300c5cfc985d2ec8e | Python | 5,903 | 220 | from nl_expr.expressions import Symbol, Constant
from nl_expr.logic import (
Implication,
Conjunction,
ExistentialPredicate,
UniversalPredicate,
)
from ..drs_builder import DRSBuilder, DRS2FOL
from ..chart_parser import ChartParser
from ..english_grammar import EnglishGrammar, EnglishBaseLexicon
import ... |
50ba9ee0e773c708964a8e4cb6c0f1cfd42c173df66956b9a576bb7f4c90685f | Python | 5,905 | 166 | import pytest
import numpy as np
from brian2 import ms, mV, defaultclock, prefs, set_device, device, seed, \
Network, NeuronGroup, StateMonitor, SpikeGeneratorGroup, Synapses
# Set working directory path such that packages and tempates can be found
# NOTE that it only works if you start the script f... |
a97cf7c330339453b88ce273e256791dda4662a827582119575e29c318be2e8e | Python | 5,907 | 184 | from __future__ import print_function, unicode_literals, absolute_import, division
from lzma import PRESET_EXTREME
import numpy as np
import warnings
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise
from ..utils import path_absolute, _is_power_of_2, _normalize_... |
aec276440eab3f3f2163aee4d4ec28127aefd4b28c2b10d372cbaf5bac7a3df4 | Python | 5,908 | 131 | import os
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.feature_extraction import FeatureHasher
import math
import torch
def load_data_from_folder(directory_ldff, filename):
dataset_train = pd.read_csv(directory_ldff + '/' + filename + '/' + 'train.csv')
panier_9999999... |
6ea7a822abe921e543ae179247d8093f38ff0471ed7111a15372652fa63e5f69 | Python | 5,910 | 122 | #!/usr/bin/env python
#######################################################################
#######################################################################
## Created on July 4th 2018 to create IGV session file from file list
#######################################################################
###########... |
18f0bffdccba0accb55e05b758cc67a2851cdb69b7e9a9471457982557778958 | Python | 5,911 | 174 | """
Adjacency matrix and incidence matrix of graphs.
"""
import networkx as nx
__all__ = ["incidence_matrix", "adjacency_matrix"]
@nx._dispatchable(edge_attrs="weight")
def incidence_matrix(
G, nodelist=None, edgelist=None, oriented=False, weight=None, *, dtype=None
):
"""Returns incidence matrix of G.
... |
f5d667faaec5e4ac9029424c89edae2b0babd851b408b5f3fe42d9ce424e8597 | Python | 5,912 | 163 | from contextlib import contextmanager
import os
from os.path import dirname, abspath, join as pjoin
import shutil
from subprocess import check_call
import sys
from tempfile import mkdtemp
from . import compat
_in_proc_script = pjoin(dirname(abspath(__file__)), '_in_process.py')
@contextmanager
def tempdir():
td... |
443a6b8275493998c8a6ff8b1abfb2bafc74fb45f6ab8c784553fa7eb0664415 | Python | 5,914 | 144 | # coding: utf-8
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"... |
c7be939e1032322d1b6bc22af65bdec8c1661d80d3b2601fcbc5713ba4baf842 | Python | 5,915 | 145 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from __future__ import annotations
from typing import TYPE_CHECKING
from ax.adapter.data_utils impor... |
695de9fe531e5f8c3be4365529715dc17694802e5512faa4624fa37221b62787 | Python | 5,919 | 77 | import tensorflow as tf
import numpy as np
import keras
import keras.backend as K
from keras.layers import BatchNormalization, Conv3D, Add, ZeroPadding3D, Lambda, concatenate
def ACBlock(input_tensor, name=None, filters=None, ksize=None, strides=(1, 1),
momentum=0.99, epsilon=0.001, moving_mean_initializer='zeros'... |
1703aac9b9a80b0894fad55abb58de1781a0f7efd1290e23aa80a6bd61528b74 | Python | 5,920 | 163 | import torch
import torch.nn as nn
import torch.nn.functional as F
from graphmae.utils import create_activation, NormLayer, create_norm
from cogdl.layers import GINLayer
class GIN(nn.Module):
def __init__(self,
in_dim,
num_hidden,
out_dim,
num_l... |
07ff5dbe8a6a20ad9677193f974375e50d3330d1d2925bbbee1b0b740417a9a0 | Python | 5,921 | 176 | import pandas as pd
import os
import sys
from loguru import logger
from brainrender.atlas_specific.allen_brain_atlas.gene_expression.ge_utils import (
check_gene_cached,
load_cached_gene,
download_and_cache,
)
from brainrender import base_dir
from brainrender._io import request, fail_on_no_connection
fro... |
08e86a481e1cfa05cb685189f4a4d89470f7ee6ae9623f8ba96e3af06fa8f3c5 | Python | 5,921 | 170 | from typing import (
Optional,
)
from pydantic import (
BaseModel,
Field,
HttpUrl,
RootModel,
)
__all__ = [
"CompositeFileInfo",
"DatatypeDetails",
"DatatypesMap",
"DatatypesCombinedMap",
"DatatypeConverter",
"DatatypeConverterList",
"DatatypeEDAMDetails",
"Datatype... |
bcded9a33777922bf21051235aa94d5cd957e9def4f43dfaf0e8fd4e44f2bbeb | Python | 5,922 | 207 | import typing
import numpy as np
from .. import config
from .._util import merge_dicts
from ..cell_types import CellType
from ..connectivity import ConnectionStrategy
from ..placement import PlacementStrategy
from ..postprocessing import AfterConnectivityHook, AfterPlacementHook
from ..rng import RngRootNode
from ..s... |
b2e8e0f386dee96c6ca00fdc3e77f562a7848e67badf8de944a67682ef0adaf1 | Python | 5,924 | 168 | import numpy as np
import pytest
from spikingjelly.datasets import shd, utils
@pytest.mark.parametrize(
("timestamps", "frames_num", "left", "right"),
[
([0, 9], 3, [0, 1, 1], [1, 1, 2]),
([4, 4], 3, [0, 0, 0], [0, 0, 2]),
([0, 1, 2], 5, [0, 0, 0, 0, 0], [0, 0, 0, 0, 3]),
([5]... |
f99de928407ac5a392f6925fe8865ed2fff73a44aed11d0b6a3628f862acdcfb | Python | 5,929 | 154 | import os.path
import pyfasta
import re
from tenkit.regions import Regions
from collections import defaultdict
import gzip
# 10X generated references that should
# have genes, regions, and snps files
KNOWN_GENOMES = ['10X_hg19_ucsc', '10X_b37', '10X_GRCh38_no_alt_decoy']
def open_reference(reference_path):
''' Op... |
5d502680df1ff4694e2440dcf9507d5e7a65de6b99fee346c1ce24b358d91da4 | Python | 5,931 | 121 | """
Determine if installed tool shed repositories have updates available in their respective tool sheds.
"""
import logging
import threading
from typing import NamedTuple
from sqlalchemy import false
from galaxy import util
from galaxy.model.tool_shed_install import ToolShedRepository
from galaxy.tool_shed.util.repo... |
b71a86e278b039ea77a2943b3ead804bb222ad28e437c379a1c22dd02e30140e | Python | 5,932 | 164 | import math
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
def auc_pair_loss(x, y, z):
x = F.normalize(x, p=2, dim=-1)
y = F.normalize(y, p=2, dim=-1)
z = F.normalize(z, p=2, dim=-1)
sim = (x * y).sum(dim=-1)
dissim = (x * z).sum(dim=-1)
loss = (1 - sim ... |
7585e3be86b9af1ed47f77dade195dd0b54a6a32ed0dfa2234c4505d52adc428 | Python | 5,933 | 186 | #!/usr/bin/python3
import matplotlib.pyplot as plt
import numpy as np
import sys
import getopt
from plotly.subplots import make_subplots
import plotly.graph_objects as go
from scipy import signal
p300folder = "p300"
class SimData:
def loadFile(self,filename):
return np.loadtxt("../{}/subject{}/{}".format(... |
27d3e7ce8e651fe01e0c96494806d49d80930ef3819ce7bb6f7e0b853906c229 | Python | 5,935 | 139 | import pytest
import tensorflow as tf
from packaging.version import parse as version
from tf_keras_vis import keras
from tf_keras_vis.saliency import Saliency
from tf_keras_vis.utils.scores import BinaryScore, CategoricalScore
from tf_keras_vis.utils.test import (dummy_sample, mock_conv_model,
... |
aab10423b1e0be20dd6a458159e46b1ebb2f9c94427e27b3d4a4382eeca8132e | Python | 5,935 | 124 | import numpy as np
from scipy.signal import savgol_filter
from fanc.tools.matrix import delta_window
import logging
logger = logging.getLogger(__name__)
def find_zero_crossing(x, sub_bin_precision=False):
diff = np.diff(np.signbit(x))
# make sure diff is not caused by nan
diff = np.logical_and(diff, ~np.l... |
f4047c04184c5695e0d777e3479497d2d4e7086f1210ded19536fc20e328399d | Python | 5,935 | 213 | # -*- coding: utf-8 -*-
"""
Parameter
=========
Provides GUI widget to parameter dictionaries used in *ClearMap* processing
routines.
The module effectively implements and interface between hierarchical
dictionaries and the parameter trees of pyqtgraph.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.... |
16d2d6073644ceb08811485251d2b8cae00098ac4700867c140916c4d881cf72 | Python | 5,937 | 141 | # Copyright (c) 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 law or agreed to in writing, so... |
a4df41e8023885e000564ece0535a7380f2dcb858be28a0504f0e2018ecd7151 | Python | 5,937 | 169 | from typing import (
Optional,
TYPE_CHECKING,
)
from galaxy.navigation.components import (
Component,
Target,
)
from .axe_results import (
AxeResults,
Impact,
)
if TYPE_CHECKING:
from galaxy.selenium.has_driver_protocol import HasDriverProtocol
class SmartComponent:
"""Wrap a Compone... |
fa8ccd265dee028d7cce09ff8d824512b85f791ea7bf249f0dd5f2e78a45e326 | Python | 5,937 | 150 | """Compute markers.
==================================================
Compute markers used for publication
==================================================
Here we compute the markers used for the diagnosis of DOC patients [1] for
an EGI recording from a control subject.
References
----------
[1] Engemann D.A.`*,... |
0ed8ecb7b2772777ec1f230e671c6d3da494e3ae7fd30211f1d7c8c79079d450 | Python | 5,938 | 135 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
3fa60c59193a886aa80b53e998baf987c68b870447f9a2991360ddf29745d4f1 | Python | 5,940 | 186 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
MEFISTO wrapper functions
Created on Mon Jul 19 18:25:31 2021
@author: townesf
"""
#import json
import numpy as np
from os import path
from time import time,process_time
#from mofax import mofa_model
from mofapy2.run.entry_point import entry_point
from utils import ... |
12d2563892c86b233663d0f99490b3fb644d2aeb6beba0182123359f11447e51 | Python | 5,941 | 265 | from operator import eq
import pytest
from nl_expr import exceptions
from nl_expr import expression_walker as ew
from nl_expr import expressions
from nl_expr import logic
from .. import Fact, Implication
from .. import negation as sdn
from ..expressions import TranslateToLogic
from ..chase import Chase as Chase_
from... |
560e241f9f6a2471ef745f3b585b66df464150d628cb88fd38422c64cae7acac | Python | 5,942 | 100 | # -*- coding: utf-8 -*-
"""
@title: Bruker_batch_convert.py
@description: script that converts each Bruker '.d' file in a directory into an '.hdf5' file containing data series and measurement metadata
@author: chrisarcadia
@created: 2018/10/29
"""
import Bruker
import timeit
import os, sys
# Provide a sour... |
0ff4c4fd22b5e586ad75b8560cc374384dd7e940899f545390034834260ea1b1 | Python | 5,943 | 178 | from __future__ import absolute_import
import email.utils
import mimetypes
from .packages import six
def guess_content_type(filename, default='application/octet-stream'):
"""
Guess the "Content-Type" of a file.
:param filename:
The filename to guess the "Content-Type" of using :mod:`mimetypes`.
... |
16f1830f5881153c0d0e189537963e98522238f6175740581a30a997c1befcba | Python | 5,944 | 163 | """
Manager and Serializer for Roles.
"""
import logging
from sqlalchemy import select
from sqlalchemy.exc import (
MultipleResultsFound,
NoResultFound,
)
from galaxy import model
from galaxy.exceptions import (
Conflict,
InconsistentDatabase,
InternalServerError,
ObjectNotFound,
RequestP... |
57d2f9f29b64b45fa92e2660d01bd43265f51bd9eea194bb2da2d7dc0d1cebb2 | Python | 5,945 | 183 | import joblib
import numpy as np
import pandas as pd
from anndata import AnnData
from scipy.sparse import issparse
from sklearn.decomposition import TruncatedSVD
from sklearn.utils.validation import check_is_fitted
def tf_idf(data, scale_factor=100000, idf=None):
sparse_input = issparse(data)
if idf is None:... |
90811ca6539513dd576c6066d2e065b9dfd34d2ab44612a528fa8e6a8f356bc3 | Python | 5,949 | 179 | import sys
import argparse
import os
from packaging import version
if "kivy_overrides" not in sys.modules.keys() and \
any([name.startswith("kivy") for name in sys.modules.keys() if
name != "kivy_overrides"]):
raise ImportError("smile must be imported before kivy")
# Prevent kivy from reading command l... |
d761c8692036631ce21717e25dddfdd26f6e4cf7115c9706252831669ad9e313 | Python | 5,949 | 164 | import pdb
import conf
import numpy as np
import torch
import torch.nn as nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
from transformers.file_utils import ModelOutput
from transformers.models.wav2vec2.modeling_wav2vec2 import (
Wav2Vec2PreTrainedModel,
Wav2Vec2Model)
from d... |
0c9ddf0795c5b16b013e55605264b3a4e0a1ca2d0d0d2c03688237a02cb2d735 | Python | 5,950 | 171 | import matplotlib.pyplot as plt # To plot
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
plt.rc('xtick',labelsize=12)
plt.rc('ytick',labelsize=12)
Dzs_all = []
Dpar_all = []
Dzs_stdv_all = []
Dpar_stdv_all =... |
8031bab6c80fdeec7b0e0bb4c7baf49eca3bff292723189c578d86ab422de697 | Python | 5,952 | 199 | import pytest
import networkx as nx
from networkx.algorithms import approximation as approx
def test_global_node_connectivity():
# Figure 1 chapter on Connectivity
G = nx.Graph()
G.add_edges_from(
[
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 3)... |
f026cdb8f208c5d3b56d033a2ebc74414ab52638968f9d9e270474d830193015 | Python | 5,955 | 155 | import sys, os, platform
from src.pnc import Environment
from src.imaging_derivs import DataVector
from src.plotting import roi_to_vtx
from src.utils import get_states_from_brain_map
import numpy as np
# %% plotting
import seaborn as sns
import matplotlib.pyplot as plt
from nilearn import plotting
from src.plotting im... |
c045a16e52ddcb589e0d49c39d6229697a0eab3129bd77ff68d9f92e406fd3bf | Python | 5,956 | 140 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Cluster the cells using the reduced matrices from dimensionality reduction
"""
import numpy as np
import os
import cellranger.analysis.clustering as cr_clustering
import cellranger.analysis.kmeans as cr_kmeans
import cellranger.analysis.pca as cr_pca
imp... |
86bf7547e2091a26e51f3ac173e9a9e31e05e3c0447a343db11b04b43d70d2e3 | Python | 5,957 | 190 | __author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'http://idisco.info'
__download__ = 'http://www.github.com/ChristophKirst/ClearMap2'
#optiimze image itme for spee... |
9e551534130615b8d3d6b5969363b4032c18fc38bc5afdaa97d882e1151df30a | Python | 5,957 | 173 | import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
import copy
def theory(d,A):
return A*d**(-2./3.)
def fitexp(d,A,b):
return A*d**(-b)
ds_main = [1,1.25,1.5,2,2.5,3,3.5,4,4... |
534edbe16b2daccea3c3c73f6eda4a283b38047358bf0c2461ba200db71ad92b | Python | 5,958 | 174 | ############################################################################## Setup
"""
ND Bayesian Optimization Test:
(0) Gaussian process model.
(1) Gemerate ND objective using BO_express autobuilding features.
(2) Test building arguements
(3) Test predictions, variance estimation, and sampling.
(4) Run single itera... |
5fc94805e9ce492d766450f1a9444d94d1ee38b1bafaffe401688af3139583ab | Python | 5,960 | 149 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Reduce the dimensions of the peak matrix
"""
import cellranger.analysis.pca as cr_pca
import cellranger.analysis.lsa as cr_lsa
import cellranger.analysis.plsa as cr_plsa
import cellranger.h5_constants as h5_constants
import cellranger.analysis.constants a... |
d1f6c7c1a907781a26b3f1e6b0827b692e4faea98033a2e41562ab558615d1cf | Python | 5,962 | 141 | import numpy as np
from ark.utils.metacluster_remap_gui.metaclusterdata import MetaClusterData
def test_can_get_mapping(simple_metaclusterdata: MetaClusterData,
simple_metaclusterdata_rename: MetaClusterData):
np.testing.assert_array_equal(
simple_metaclusterdata.mapping['metaclu... |
55a1dab6ac0eb9a798b2ebbf50068cc4ad0f83f3331a94ad355250805dd98c06 | Python | 5,963 | 215 | from copy import deepcopy, copy
import re
# An expression tree node
class Et:
# Constructor to create a node
def __init__(self, value):
self.value = value
self.left = None
self.right = None
# Returns root of constructed tree for given postfix expression
def construct_exp_tree(postfix... |
d087a7e1edd01dd9a70104cc831afad5b31ec7a7e83e79a8fdee608e2696972b | Python | 5,968 | 170 | import pytest
import networkx as nx
@pytest.mark.parametrize("n", range(1, 6))
def test_chordal_graph_clique_ignores_selfloops(n):
"""The one and only chordal graph clique of a complete graph K_n is the
set of n nodes. Ensure this is the case even when self-loops are present."""
G = nx.complete_graph(n)
... |
f0af112b3f038dcadc8f7506d53de62c8270f90b18b6f3fb58cc039937509f3b | Python | 5,968 | 140 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
"""
from __future__ import division
import os
import h5py as h5
import martian
import tables
from scipy.sparse import vstack
import pandas as pd
import numpy as np
import cellranger.h5_constants as h5_constants
import cellranger.io as cr_io
import cellra... |
2876afe697006d1e860efb0326662ae9de21c8334cce9aa627360e53db6d970b | Python | 5,969 | 195 | import os.path as osp
from collections import defaultdict
import numpy as np
import scipy.sparse as sp
import torch
from cogdl.data import Dataset, Graph
from cogdl.utils import download_url, untar
def read_cf_amazon(file_name):
return np.loadtxt(file_name, dtype=np.int32) # [u_id, i_id]
def read_cf_yelp2018... |
97cb21c601da61af723f3c52f6a69868a810ea54ed96ba54bd3eebf7689e6e16 | Python | 5,972 | 159 | import contextlib
import unittest
from unittest import mock
import numpy as np
import requests
from bsb_test import (
FixedPosConfigFixture,
NumpyTestCase,
RandomStorageFixture,
skipIfOffline,
)
from scipy.spatial.transform import Rotation
from bsb import FileDependency, NeuroMorphoScheme, Scaffold, U... |
ff3dd5afedca1640a001a2bd87aecb7c3969aa7604adf70fad66a5de8e93c17b | Python | 5,972 | 198 | import contextlib
import importlib.metadata
import json
import os
import shutil
import warnings
from datetime import datetime
from pathlib import Path
import shortuuid
from ... import config
from ...exceptions import BsbProvenanceUpgradeWarning
from ...services import MPILock
from ..decorators import on_main_until
fr... |
6a0210ccf556957b570e2560e825af0f3ac4178655c6105ca27695ec893bd313 | Python | 5,974 | 157 | import io
import pickle
import sys
import time
from tqdm import tqdm
from src.gsfsf import *
from src.pre_data import *
from src.train_and_evaluate import *
from src.warmupLR import *
import warnings
warnings.filterwarnings("ignore")
USE_CUDA = torch.cuda.is_available()
size_split = 0.8
PAD_token =... |
be74a96a45cc537945885c725f7b2d5b34f2bb63a75861bc280dab74e95cac16 | Python | 5,974 | 164 | from __future__ import absolute_import
import datetime
import json
import logging
import os.path
import sys
from pip._vendor import lockfile, pkg_resources
from pip._vendor.packaging import version as packaging_version
from pip._internal.index import PackageFinder
from pip._internal.utils.compat import WINDOWS
from ... |
f7678f5bdaf845a6086fb4a910dd2e0ed135316e39d65d488922aeedf5c6c7f1 | Python | 5,975 | 177 | """
Compare numpy vs GPU backend on a real video stimulus.
Downloads a short demo video, extracts motion energy features using both
numpy and a GPU backend (torch_mps or torch_cuda), and saves the results.
Usage::
python benchmarks/compare_numpy_vs_gpu.py
python benchmarks/compare_numpy_vs_gpu.py --backend t... |
a8b65fa884096850e2c5027a2c5961385205b21b2bb93c67efaf3413bcebb122 | Python | 5,977 | 157 | #!/usr/bin/env python3
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
from collections.abc import Callable
from typing import Any
import numpy as np
import numpy.typing as... |
c8bd26ab9c03efe4e8306cbcf032f8dc6f54fcd7bde0440836ff50a4b55751d0 | Python | 5,977 | 152 | """Asynchronous Fluid Communities algorithm for community detection."""
from collections import Counter
import networkx as nx
from networkx.algorithms.components import is_connected
from networkx.utils import groups, not_implemented_for, py_random_state
__all__ = ["asyn_fluidc"]
@not_implemented_for("directed")
@n... |
dcaa8fef4968a23824f0b0bd295cdfd37f0397672c49b1ff53d7bfbe4060a555 | Python | 5,977 | 163 | import time
import networkx as nx
import numpy as np
import scipy.sparse as sp
from sklearn import preprocessing
import torch
import torch.nn as nn
import torch.nn.functional as F
from tqdm import tqdm
from .. import BaseModel
class DNGR_layer(nn.Module):
def __init__(self, num_node, hidden_size1, hidden_size2)... |
b1a2c66f73c6b955c15ae4ce60925ddad74e31e6091ecb10f7cd01135b12a4ff | Python | 5,978 | 238 | import dataclasses
import itertools
import typing
from ._util import MechId
from .definitions import (
CableProperties,
CableType,
Definition,
Ion,
Mechanism,
Synapse,
_parse_dict_def,
)
class Constraint:
def __init__(self):
self._upper = None
self._lower = None
... |
b245ac61f75e55f50f3c6e805505c9b68aa8dd16a9d6dcfed125d4af5892d37b | Python | 5,978 | 168 | #!/usr/bin/env fbpython
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# pyre-strict
import functools
import time
from collections.abc import Callable, Sequence
from logging import WARN... |
722166c6f190d4b2011dff449834b5b0960df054c9c82f550ab7511e357b5c72 | Python | 5,982 | 121 | from __future__ import annotations
import dask.array as da
import numpy as np
import pytest
import xarray as xr
from squidpy._params import resolve_params
from squidpy.experimental.im._stain._constants import RUIFROK_HE
from squidpy.experimental.im._stain._conversion import sda_to_rgb
from squidpy.experimental.im._st... |
89090115c28ee46316fc234d49d3f37c44dc48d852e6648a9f7ed74de42878ff | Python | 5,985 | 164 | import copy
import random
import numpy as np
import torch
from .. import ModelWrapper
class GCNMixModelWrapper(ModelWrapper):
"""
GCNMixModelWrapper calls `forward_aux` in model
`forward_aux` is similar to `forward` but ignores `spmm` operation.
"""
@staticmethod
def add_args(parser):
... |
26f23225b9ac06654419f5644c451526a70b5c77001709d281be76c17e2a13b0 | Python | 5,987 | 177 | import logging
import numpy as np
from scipy.spatial import distance as dist
from sklearn.base import BaseEstimator
from sklearn.manifold import SpectralEmbedding
from sklearn.utils.validation import check_is_fitted
from divik.core import configurable
from divik.core.io import save_csv
@configurable
class LocallyAd... |
57f604ba9ae0d9657b5453673c3dc34fba8ad50b68c90d49a7ed0e7f958328ab | Python | 5,987 | 127 | import numpy as np
import sys
import matplotlib.pyplot as plt
def read_dist_xvg(fname):
dat = [[], []]
with open(fname) as fhandle:
for line in fhandle:
if not (line.startswith('#') or line.startswith('@')):
recs = line.strip().split()
dat[0].append(float(rec... |
8daaa91930e603255279b015e8f3b6a3a312f1a4ced04094e81e3bdfdd201cb9 | Python | 5,987 | 165 | """
Serve the REPL in the browser on this machine.
The page (``doc/_static/repl``) is static: Python runs in the browser, on
Pyodide. This script puts it, with the logo, in SITE, builds its bundle
there with ``make_repl_bundle.py`` (NeuroLang's wheels and the engine's
data; once, or again with ``--rebuild``, or from n... |
92477625f575d23d164fd2db96f2e254b6a527df4a0dc209a862440844049a8e | Python | 5,987 | 122 | # -*- coding: utf-8 -*-
from figureflow import figure
import seaborn as sb
from matplotlib import pyplot as plt
import importlib
import numpy as np
importlib.reload(figure)
import os
Figure = figure.Figure
# get the path to the data of the respective figure or movie
# the data is in the data folder in a folder with ... |
df383ac6f192204a3707709a841603de1ff31e8ed159ab8fdb1a9c00d4c1e938 | Python | 5,987 | 177 | """**Depricated**. Will be removed in a future version."""
import os.path
import numpy as np
import pickle
import warnings
def save(data, path = "", var_name = "data", max_depth = 2, ending = None):
"""
**Depricated**. Will be removed in a future version. Saves data using the legacy data manager. Allows for ... |
39f7a5158ccf9f11a55376a6133f6e04b8c204eae2c20261e100bf696f521775 | Python | 5,991 | 150 | from __future__ import absolute_import
from .filepost import encode_multipart_formdata
from .packages.six.moves.urllib.parse import urlencode
__all__ = ['RequestMethods']
class RequestMethods(object):
"""
Convenience mixin for classes who implement a :meth:`urlopen` method, such
as :class:`~urllib3.con... |
bf178da3af49335951f68d0c5b75e8bf5a76d1f381288a0b51539708b41a107d | Python | 5,992 | 155 | """Tests alternate OBOReader."""
import sys
import timeit
import datetime
# Test local version of goatools
sys.path.insert(0, '..')
from goatools.obo_parser import GODag
#################################################################
# Sub-routines to tests
#########################################################... |
e7605b30c45ac4acb5a99341a7cee5019a3d797b063e5d7f4e1d31c66d9f1730 | Python | 5,992 | 171 | """
Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import os
import numpy as np
from tqdm import trange
import matplotlib.pyplot as plt
from pathlib import Path
import torch
from cellpose import models, metrics, io, transforms, denoise
# uses tensorflow
# pip i... |
bc37665ba634f69bd32d5b4fc74077cdedeefb9f61d66a6959accd2b796b0d1c | Python | 5,993 | 162 | from sqlalchemy import (
false,
select,
)
from galaxy import model
from galaxy.exceptions import (
Conflict,
ObjectAttributeMissingException,
ObjectNotFound,
RequestParameterInvalidException,
)
from galaxy.managers.context import ProvidesAppContext
from galaxy.model import Group
from galaxy.mod... |
e1beebd2c197f494c8b499289ff865d8c8490787f4dbb186c9435ac897a28c63 | Python | 5,993 | 145 | from __future__ import print_function
import argparse
import numpy as np
import torch
import torch.optim as optim
import torch.utils.data as data_utils
from torch.autograd import Variable
from dataloader import MnistBags
from model import Attention, GatedAttention
# Training settings
parser = argparse.ArgumentParse... |
d9e0ca85937c20f8490757b1b94d15a355a5eac9e321d67eb4aecdd12993a0df | Python | 5,994 | 151 | """Command-line interface for the Voluseg pipeline.
Installed as the ``voluseg`` console script; ``app/app.py`` keeps the
container entry point (``python3 /voluseg/app/app.py``) working.
"""
import json
from typing import Annotated, Optional
import typer
app = typer.Typer(add_completion=False)
def _version_callba... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.