sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d278d54552f55dc2ae7a17ed62298be2aab1528508b60ac9136462b9ecfc6001 | Python | 7,170 | 194 | import logging
import os
import subprocess
import time
from dataclasses import dataclass
from string import Template
from typing import (
Any,
Optional,
)
from typing_extensions import Protocol
from galaxy.util import (
RWXR_XR_X,
unicodify,
)
from galaxy.util.resources import resource_string
from ..f... |
6008f28240337708042b6cf03264ef12b4e65dd2a3de48b2c277c0e17749e8aa | Python | 7,175 | 143 | # For more documentation see vert_int_method_variability.ipynb
import os
import xarray as xr
import numpy as np
## Set by the user ##
GRID_RES = 'R02B05' # Can be 'R02B05', 'R02B04'. Relevant for both the input and the output grid.
SOURCE = 'NARVAL' # Can be 'NARVAL', 'QUBICC', 'HDCP2'. To set paths, inpu... |
8eb844d36b73ebf8e32184ce4a7988c65c951032bfce843bb86f0393d545ba18 | Python | 7,175 | 167 | import seaborn as sns
import pandas as pd
import numpy as np
import scipy
from matplotlib.font_manager import FontProperties
import functools
class RegressionPlot():
CONTINUOUS_X = True
def __init__(self, x, y, hue, data, plot_colors,size_factor, ax,
show_formula=True,
positi... |
b6215600acbca2458d4aae66bdc0cf652f9ea53629d811e88965c7ba5de28d34 | Python | 7,175 | 181 | import pathlib
from typing import List, Union
import numpy as np
import xarray as xr
from alpineer import misc_utils, image_utils, load_utils
from ark.segmentation.ez_seg.ez_seg_utils import log_creator
def composite_builder(
image_data_dir: Union[str, pathlib.Path],
img_sub_folder: str,
fov_list: list[st... |
96cf567d0041df06e8ec3893279c88985f53d787b6ab8c4d78ea7b8584122be3 | Python | 7,181 | 213 | """
Line editing of the interactive REPL.
It provides the completion of predicates, their columns and the
Datalog and SQUALL grammars (:class:`~.completion.NeuroLangReplCompleter`),
syntax highlighting (:class:`NeuroLangLexer`), the bottom toolbar,
suggestions from the history and the vi and emacs editing modes
(``.mo... |
6692349d4a26e30ced432f80b1205c8c3665fd335a9702284fdebc8fd44072b9 | Python | 7,182 | 155 | # -*- coding: utf-8 -*-
import pandas as pd
import os
import re
import copy
import numpy as np
import time
def goDeeper(props,this_path,a,max_a,conditions,folders):
a += 1
for newFolder in os.listdir(this_path):
print(newFolder)
if conditions[a-1] != "":
if newFolder... |
88784f33d0a22b708a30dc5ada906f0cd0d89cd35c5a28108aac3ac067cdeab0 | Python | 7,183 | 196 | import pickle
import os
import pandas as pd
from tqdm import tqdm
import numpy as np
import matplotlib.pyplot as plt
import json
from csv import reader
from utils.Utils import *
from .models import *
base_url = 'scheduler/src/'
def one_hot(value, lst):
vec = torch.zeros(len(lst))
vec[lst.index(value)] = 1
return v... |
e2f4547dcd4309a441e94336dc4b1b485981dcba4af82716d8af85b30ce96edf | Python | 7,186 | 142 | import unittest as ut
import networkx as nx
from pysbm.sbm.hierarchical_inference import HierarchicalInference
from pysbm.sbm.hierarchical_inference import PeixotoHierarchicalInference
from pysbm.sbm.nxpartitiongraphbased import NxHierarchicalPartition
from pysbm.sbm.peixotos_hierarchical_sbm import LogLikelihoodOfHi... |
a3c4f609fbfc118374d2c3b833404b9b243911c35fdb0db0b65112873e5ffa4d | Python | 7,187 | 173 | #!/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 time import time
from typing import TYPE_CHECKING
import pan... |
c7e1f3782ae9e1fcf5643276d5581fd3bf138973eb680557a889077f04b37b16 | Python | 7,188 | 188 | import torch
import torch.nn.functional as F
from torch_geometric.nn import SAGEConv, GCNConv, GraphConv, TransformerConv
class BaseGNN(torch.nn.Module):
def __init__(self, dropout, num_layers):
super(BaseGNN, self).__init__()
self.convs = torch.nn.ModuleList()
self.dropout = dropout
... |
8d30ae00806f8f2d20336f59a9de7349353953d37807a3130bfa38ca23d3ad40 | Python | 7,189 | 269 | import pynwb
from contextlib import contextmanager
from datetime import datetime
from dateutil.tz import tzlocal
from uuid import uuid4
import numpy as np
@contextmanager
def open_nwbfile_local(file_path: str):
"""
Context manager to open and close a local NWB file.
Parameters
----------
file_pat... |
e4129e3a24e2f9cf62e275bc7f66cb771ea6ab3de262abea8fc4c4b22bc06f49 | Python | 7,190 | 206 | import numpy as np
import scipy.sparse as sp
import torch
import torch.nn as nn
from .. import BaseModel
from .dgi import GCN
from cogdl.utils.ppr_utils import build_topk_ppr_matrix_from_data
from cogdl.data import Graph
def sparse_mx_to_torch_sparse_tensor(sparse_mx):
"""Convert a scipy sparse matrix to a torch... |
938a58e8e2332fbe2e04cc6b995b0213e90a4cacf9bf1413b303ff11f8fcb233 | Python | 7,193 | 177 | # MIT License
#
# Copyright (c) 2019-2024 The PyQMC Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, m... |
db741db3f884bda9c1d6cbf625c79dbdaea9430fd92b3c20ba9352fb2845b09b | Python | 7,195 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
6e418bceb41344695c07e416e589dd7cc8aaca854454535f50e331252ba5f532 | Python | 7,196 | 194 | # This file is NOT licensed under the GPLv3, which is the license for the rest
# of YouCompleteMe.
#
# Here's the license text for this file:
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is free to copy, modify, publish, use, compile, sell, or
# distribute this software, either... |
9bcbaf42eec92c9636de205b1ee93e317e3ad95f018d0a7c88b21f8ab8da2f4a | Python | 7,198 | 231 | import pyinspect as pi
from io import StringIO
from rich.console import Console
import numpy as np
from myterial import orange, salmon, amber
from vedo import Text3D, Sphere
from brainrender._utils import listify
# transform matrix to fix labels orientation
label_mtx = [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0,... |
fd70993f95c779a20ec65a0aa6cdd238694b9bcb53ce570f7d98e7b58f37b423 | Python | 7,198 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
a17c180cba38f3840d80b3d9320ef81f50043b15fc5c48ced5a73d01f82c0e92 | Python | 7,200 | 158 | import time
import networkx as nx
import numpy as np
from sklearn import preprocessing
from tqdm import tqdm
from cogdl.utils import alias_draw, alias_setup
from .. import BaseModel
class LINE(BaseModel):
r"""The LINE model from the `"Line: Large-scale information network embedding"
<http://arxiv.org/abs/15... |
a8f0184057969fe73201e895ced1a80a2608701e51fa858bb6d13ad1164fa8a3 | Python | 7,201 | 161 | from math import fabs as fabs
from math import floor as floor
from math import sqrt as sqrt
from scipy.special import erfc as erfc
from scipy.special import gammaincc as gammaincc
from numpy import zeros
class RunTest:
@staticmethod
def run_test(binary_data:str, verbose=False):
"""
The focus o... |
ed618d116c5000097486b481a2d2766d2df72324b0a51c0d6cb27a71888f83bf | Python | 7,203 | 211 | #!/usr/bin/env python3
import os
import subprocess
import sys
import yaml
from bids import BIDSLayout
import bids
from glob import glob
from snakemake import snakemake
import argparse
import json
bids.config.set_option('extension_initial_dot', True)
# create a keyvalue class for accepting key=value pairs in argparse
... |
fd253b24437325948b7ebed786d9afba454663606a141a973420ef67deca3f0d | Python | 7,205 | 222 | from __future__ import annotations
import re
from functools import partial
from typing import TYPE_CHECKING
import h5py
import pandas as pd
import pytest
import scipy.sparse as sp
import zarr
from zarr.storage import MemoryStore
import anndata as ad
from anndata.compat import CSArray, CSMatrix
from anndata.experimen... |
1e1da8ec160468ae4f4f7b72977a1e01652478a13762afa963b2e3de210b0fd4 | Python | 7,211 | 191 | """Provide constants for several settings in the experiment."""
import os
from collections import OrderedDict
import numpy as np
# MASTER SETTINGS
# Set number of participants to record for your study. Must be divisible by 4
n_participants = 40
# Now define a function to create the experimental design for us
def pr... |
f375dd5f005d25bec0ab0c8a52395b709efe3546a410765c90ea52385b6b3ade | Python | 7,214 | 199 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import time
import dgl
import numpy as np
import torch
import torch.nn.functional as F
from dgl.data import register_data_args
from pytorch_lightning.metrics.classification import Accuracy
from pytorch_lightning.metrics.functional import auro... |
ee05d59169c053e75aeb9f1a35af8228dbeaafec6931d1161ebd80e30e52c721 | Python | 7,218 | 194 | #!/usr/bin/env python3
import os
import numpy as np
# -custom-written code
import main_task_free
import utils
from params.param_stamp import get_param_stamp_from_args
from params.param_values import check_for_errors,set_default_values
from params import options
from visual import visual_plt as my_plt
## Parameter-val... |
bf9a4cb6ab269d9e5ed9c9fd6fad88be196475be7bc0a4f4a47d67dced59480b | Python | 7,221 | 194 | """Graph utilities."""
from __future__ import annotations
from collections.abc import Sequence
from contextlib import contextmanager
from typing import Any
import numpy as np
from anndata import AnnData
from anndata.utils import make_index_unique
from pandas import CategoricalDtype, Series
from pandas.api.types impo... |
d889a51fdacfc1c44bf4b7c508024b1b78d74312cb14a1b065bdcfa8b2931e20 | Python | 7,221 | 195 | #!/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 ax.core.arm import Arm
from ax.core.experiment_status import ExperimentStatus
from ax.core.genera... |
093cf3297c1b95ac8a712e968f0ec81ddc243f05d39f9079cb984adea37e3afb | Python | 7,225 | 225 | # 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... |
a85216cb988a3f5490d8b67b7da6ad08d45df370138c53eab17805fc8c161a79 | Python | 7,225 | 172 | # 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... |
4469bf5700a83bcaff0abb04fe08f27353253bf7be2f1219f88ff1b2b0fd934e | Python | 7,226 | 193 | import torch
import torch.nn as nn
from .. import base, functional
__all__ = ["STBIFNode"]
def _as_scalar_tensor(value) -> torch.Tensor:
tensor = value if torch.is_tensor(value) else torch.tensor(value)
return tensor.detach().clone()
class STBIFNode(base.MemoryModule):
def __init__(
self,
... |
96d1174ac4d3a2bbfeb2cfef2871ff915e7ae60dd990eac0f9a40bea58166bbc | Python | 7,228 | 246 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
f84eb02e415233d3e352d10888a4011661ed6d21ec4344b77ea30cff9ccb8a33 | Python | 7,232 | 195 | import sqlite3
from contextlib import contextmanager
from functools import lru_cache
from typing import (
NewType,
Optional,
)
from sqlalchemy import create_engine
from sqlalchemy.engine import Engine
from sqlalchemy.engine.url import make_url
from sqlalchemy.orm import object_session
from sqlalchemy.sql.compi... |
f756f5a5ed0a1b1ca2ed2650788ca3038f881735b15683f926041c8fe4ce6a6e | Python | 7,235 | 111 | import time
import numpy as np
import matplotlib.pyplot as plt
import figplot
t1 = time.time()
conv_time = 200000
def plot_timeseries_sd_two(g_1, g_2, g_sd_1, g_sd_2, g_min, g_max, t_min, t_max, aspect, fig, plot_x, plot_y, plot_area):
time_trace = np.arange(t_min - conv_time + 1, t_max - conv_time + 1)
ax... |
565a0e66d2824fea9727df4f4d2e84f9c6d02771ca43dad0539cb616f99d0025 | Python | 7,237 | 188 | import collections
import json
import logging
import os
import string
from typing import Optional
from galaxy.app_unittest_utils.tools_support import UsesTools
from galaxy.config_watchers import ConfigWatchers
from galaxy.model import tool_shed_install
from galaxy.model.tool_shed_install import mapping
from galaxy.too... |
169382a5585d902176a9f3e72316990c711336eb6fb9288b831e9771e41e20d6 | Python | 7,239 | 241 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
337fa08af8cec8d91cea6498932e3f2ea53267bad2c0408cdaa915987ef676ba | Python | 7,239 | 186 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_sparse import spspmm
from .. import BaseModel
from cogdl.layers import GCNLayer
from cogdl.utils import remove_self_loops, coalesce
class GTConv(nn.Module):
def __init__(self, in_channels, out_channels, num_nodes):
... |
e0b099f63723a637a705f776faa4de67e41b47410a1555ebbd6601e5b9d84b57 | Python | 7,239 | 141 | import os
import numpy as np
import nibabel as nb
import shutil
import glob
import argparse
from os.path import join as opj
from meld_classifier.tools_commands_prints import get_m, run_command
def merge_predictions_t1(subject_id, t1_file, prediction_file, output_dir, verbose=False):
''' fusion predictions and t1
... |
2e66f8bee4978c72e5c33b4de19974fb547f6918477127ad7fd3c9246011d809 | Python | 7,240 | 243 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
fb0a56e8c5468911ec45a5220d1d5211375a6ed2a384157fc6af00ce27ab36fa | Python | 7,241 | 142 | #!/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
from ax.utils.common.testutils import TestCase
from ax.utils.measurement.synthetic_... |
7093a22e7a0cf05bec121bc88451df96aef3bb6f70d4d8cb9d435953e6c0fe79 | Python | 7,242 | 231 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 5 11:24:49 2020
@author: amelie
"""
from brian2 import *
from scipy import signal
from cells.RS_FEF import *
from cells.FS_FEF import *
from cells.SI_FEF import *
from cells.VIP_FEF import *
from FEF_visuomotor import *
from FEF_contrast_detecti... |
10dcae8be9aa0c54b5b5137d642e8bf18bb407fd0a585d59f0622e0282831b7c | Python | 7,245 | 182 | import torch
import numpy as np
import pandas as pd
def load_data(x_path, y_path):
Y = np.genfromtxt(y_path, delimiter=",")
X = np.genfromtxt(x_path, delimiter=",")
## scale each SNPs to have unit variance
for i in range(X.shape[1]):
X[:,i] = X[:,i] - np.mean(X[:,i])
Y = (Y - np.mean(... |
bcc8c68b4e50fd6c11fc7d028d96dc8b0cc4bda862f8028bd58c84c907709067 | Python | 7,247 | 200 | # -*- coding: utf-8 -*-
# Author: Florian Boudin
# Date: 09-11-2018
"""Single Topical PageRank keyphrase extraction model.
This implementation is an improvement on a keyphrase extraction algorithm,
Topical PageRank (TPR), incorporating topical information from topic model and
described in:
* Lucas Sterckx, Thomas De... |
2d7433e714973417b3397316fbb088492e1deeff79734d3083b3376e28d2ac90 | Python | 7,251 | 183 | import hashlib
import logging
from typing import Optional
from galaxy import exceptions
from galaxy.files import (
ConfiguredFileSources,
FileSourcePath,
ProvidesFileSourcesUserContext,
)
from galaxy.files.models import FilesSourceOptions
from galaxy.files.sources import PluginKind
from galaxy.managers.con... |
3145f5eca521d51b595aedd1541b74426d7c98b46ace40fed6d5438af871207b | Python | 7,252 | 209 | from typing import List, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from cogdl.data import Graph
from cogdl.layers import GCNLayer
from cogdl.utils import dropout_adj, get_activation
from torch_sparse import spspmm
from .. import BaseModel
class Pool(nn.Module):
def __init__(
... |
c2c30312d1d5dbdacc520319f86dca4ff6169dc97a080bf3dcad5fa2276ea27f | Python | 7,253 | 217 | from oct.utils import *
import logging
from ..load.metadata import Metadata
cp, np, convolve, gpuAvailable, freeMemory, e = checkForCupy()
class Structure:
""" Structure contrast OCT reconstruction """
def __init__(self, mode='log'):
acceptedModes = 'log+linear'
if mode in acceptedModes:
... |
79e1de663147969290cd3260e7bc376bd88136a7de16ce115ee8292d80bb3981 | Python | 7,254 | 224 | import pytest
import networkx as nx
class TestConfigurationModel:
"""Unit tests for the :func:`~networkx.configuration_model`
function.
"""
def test_empty_degree_sequence(self):
"""Tests that an empty degree sequence yields the null graph."""
G = nx.configuration_model([])
a... |
3afcfbe434302274769749fc2a37818556a635a97d8fad762233fc43f45c8cb0 | Python | 7,256 | 209 | """Functions for computing reaching centrality of a node or a graph."""
import networkx as nx
from networkx.utils import pairwise
__all__ = ["global_reaching_centrality", "local_reaching_centrality"]
def _average_weight(G, path, weight=None):
"""Returns the average weight of an edge in a weighted path.
Par... |
ad82c29a99e51ed93047fc824dc6b969f2ea82eb27995f5c4828a9ce06c17a70 | Python | 7,257 | 111 | import time
import numpy as np
import matplotlib.pyplot as plt
import figplot
t1 = time.time()
conv_time = 200000
def plot_timeseries_sd_two(g_1, g_2, g_sd_1, g_sd_2, g_min, g_max, t_min, t_max, aspect, fig, plot_x, plot_y, plot_area):
time_trace = np.arange(t_min - conv_time + 1, t_max - conv_time + 1)
ax... |
57fb0265f6bbed5695e1beb53c81f0f7bc9ad6914ea8a105950fc38968798a1c | Python | 7,259 | 216 | """
spaln Composite Dataset
"""
import logging
import os.path
from collections.abc import Callable
from typing import (
Optional,
)
from galaxy.datatypes.data import Data
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import (
DatasetHasHidProtocol,
DatasetProtocol,
... |
2bbfa934957b43b75e9fb945086600977d65d12bb6ca30664d9c072e77555e68 | Python | 7,260 | 242 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
615184d64d1f01d3dffa081c72e6cb35551b466eb8740db775bbb9249f21c59f | Python | 7,261 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
7b9e81ba6ae534276252025c63e197c0691ef169fc3dc876cacd94cdf6cdf889 | Python | 7,261 | 238 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 6 18:10:06 2021
@author: townesf
"""
import pathlib
import numpy as np
from math import ceil
from copy import deepcopy
from dill import dump,load
from pandas import read_csv as pd_read_csv
from tensorflow import clip_by_value
from scipy.sparse impo... |
751e51e09591cd12790990c916ba0c73c000cff55c3ceff5a59744e098498578 | Python | 7,262 | 191 | """
Tests for Robust Single Linkage clustering algorithm
"""
# import pickle
import numpy as np
from scipy.spatial import distance
from scipy import sparse
from sklearn.utils.estimator_checks import check_estimator
from hdbscan import RobustSingleLinkage, robust_single_linkage
# from sklearn.cluster.tests.common impor... |
0893ebc8a075d35876347b37bfe018dfb928a1644ae8ecc2487db708838f30e7 | Python | 7,265 | 169 | import os.path
import shutil
import sys
import numpy as np
import tensorflow as tf
import pickle
from nets import nets
def get_dataset_handlers(opt, opt_datasets):
# Initialize dataset and creates TF records if they do not exist
datasets = []
test_datasets = []
test_iterators = []
if opt.dataset.d... |
901aac32a8a9337d7491433b0e40315583730f7994bd41357b6598eed4a2247b | Python | 7,269 | 247 | """
This module includes the main class that handles the computation
of the NH-order parameters.
"""
# Python import(s).
import numpy as np
# Private import(s).
from src.chemical_shifts.auxiliaries import ACCEPTED_RES
class NHOrderParameters(object):
"""
This class computes and returns the "S^2" NH order
... |
0215f676a48453858ed3e434b5951f08fc95c7032c57d5c9bfabf1efcf399c6f | Python | 7,273 | 245 | # -*- coding: utf-8 -*-
"""
Parallel tools for writing and reading large data arrays.
This module provides parallel reading and writing routines for very large files.
"""
__author__ = 'Christoph Kirst <ckirst@rockefeller.edu>'
__license__ = 'MIT License <http://www.opensource.org/licenses/mit-license.php>'
__copy... |
8991e4c927e25c9fc2633fed9670371746b95a925073ab94cf8b2fd675f1eb7b | Python | 7,276 | 200 | from __future__ import division
from fanc.architecture.architecture import calculateondemand
from fanc.architecture.genome_architecture import MatrixArchitecturalRegionFeature, VectorArchitecturalRegionFeature
from fanc.data.genomic import GenomicRegion, Node, Edge
import tables as t
import types
import numpy as np
c... |
6b9872829d56efc8b490ad5f61f7b255c7f03fc1d334ddafb857c83dad5c09dc | Python | 7,278 | 188 | # 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 typing import Any, final
import pandas as pd
from ax.adapter.base import Adapter
from ax.analysis.analysis import Analy... |
fb30f0e0ed544eddb4f1e34ca08f34d94c9eedef0676bf65b5502da1609ca1b7 | Python | 7,280 | 162 | # Copyright 2020 DeepMind Technologies Limited.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... |
6d2fc12410068538574e616e718ac6b928392879cb1357e2e866b16807b3ba86 | Python | 7,282 | 263 | # -*- coding: utf-8 -*-
"""
SMA
===
Shared memory arrays for parallel processing.
Note
----
Usage of this array can help for parallel processing of shared memory
arrays. However, using memmap sources (:mod:`~ClearMap.IO.MMP`) often enable
faster implementations.
"""
__author__ = 'Christoph Kirst <christoph.kirst.... |
8eb82b8a7d7d33ade35dff26645a978556b922823ac2b546353a9b682bd5fb11 | Python | 7,282 | 225 | """
Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import time
import numpy as np
from tqdm import trange
import matplotlib.pyplot as plt
from pathlib import Path
from cellpose import transforms, io, metrics
from cellpose.models import CellposeModel
# uses torc... |
9df1fdb5d5ddd27092aeeea0d218c28931bc4b732bf734bc193bef5cc55fd02b | Python | 7,282 | 205 | # -*- coding: utf-8 -*-
"""
Created on Fri Jun 10 11:03:57 2022
@author: Estefany Suarez
"""
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import os
import itertools as itr
import numpy as np
import pandas as pd
from scipy import stats
#%%
RESOLUTION = '100'
PROJ_D... |
ad424d6bfda72834a4ef9160d72ca030f02a83f05d93480658c0d1298f20d659 | Python | 7,282 | 213 | import random
import pytest
import networkx as nx
from networkx.algorithms.link_analysis.pagerank_alg import (
_pagerank_numpy,
_pagerank_python,
_pagerank_scipy,
)
from networkx.classes.tests import dispatch_interface
np = pytest.importorskip("numpy")
pytest.importorskip("scipy")
# Example from
# A. La... |
60acacdae3e88e07d4216df0a4ee13626bc87bd81976ef0cca688afe7e2151d4 | Python | 7,286 | 184 | from typing import Generator, List, Union
from skimage.io import imread
from alpineer.image_utils import save_image
from alpineer import io_utils
import os
import re
import shutil
from tqdm.auto import tqdm
import numpy as np
import pathlib
import pandas as pd
def find_and_copy_files(mask_names: List[str], source_fol... |
03a351010c203c5820bccae3d350baf7b42ac41273df9a1e27f62ef889f346c7 | Python | 7,291 | 187 | """ HCBS Pruning Network Inference """
import torch
import numpy as np
from ...types import bbox
from ... import seg_utils
from . import locs
def prune_candidates(net, img, seg, patchsz, candidates, cleft=None,
output_thresh=0, cleft_locs=None, prox=None,
cleft_ids=None, l... |
b115208bf0a241e03db0952fb579a95422795e8277657077c4e5bee737abcd06 | Python | 7,291 | 239 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 6 18:10:06 2021
@author: townesf
"""
import pathlib
import numpy as np
#from pickle import dump,load
from math import ceil
from copy import deepcopy
from dill import dump,load
from pandas import read_csv as pd_read_csv
from tensorflow import clip_b... |
b24a87189a653f030734d154743b22ee3ca4b0391df63384bd7c222a0e0b904a | Python | 7,292 | 182 | import numpy as np
from ... import config
from ...config import types
from ...connectivity.strategy import roi_key
from ...trees import BoxTree
from .. import ConnectionStrategy
from ..strategy import Hemitype
from .geometric_shapes import ShapesComposition
@config.node
class ShapeHemitype(Hemitype):
"""
Cla... |
3709b61b07a9852276971beeb53d6764ff6f13cccef3cd9c0a0abd338d752925 | Python | 7,294 | 158 | """ heavy-lifting workflow functions"""
# General I/O
import os
import subprocess
import time
# fishdot
from helpers_and_sources import generators, image_augmentations, image_operators, image_segmentation_model
# segmentation
from tqdm import tqdm
import tifffile as tf
import numpy as np
import torch
def print_cur... |
df38f207f70eee5b4218a6a5f18460f72748df90e0f396964dee6bcf89e4b59b | Python | 7,294 | 181 | import numpy as np
from skimage import filters, measure, morphology
from skimage.segmentation import watershed
from GeneralFunctions import upper_inner_fence
def seeded_watershed(input_binary, input_represent, t, min_seed):
"""
Seeded watershed to further split undersegmented objects,
input... |
3494eb389361595844348b5152e5ad9ddb5e6007c9d7d692ce9a4cf41a672476 | Python | 7,297 | 242 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
08349e1cbe7f1a37af5923947afb1d1b1d6e35d4242c9c81baca9aa2b450a395 | Python | 7,298 | 237 | import torch
import triton
import triton.language as tl
from triton.language.extra import libdevice
from ..triton_layout import (
_block_minor,
_neuron_grid,
_neuron_indices,
_spatial_offsets,
_time_offset,
_triton_layout_args,
)
from .autograd import _check, _check_backward
@triton.jit
def _... |
69efd72c6ff9300ace3ead7584545420f90a2847e04e46d2a7518aef0eb6f4cb | Python | 7,298 | 210 | """
Created on Dec 30, 2020.
Implements a convenient data handler for large, unbalanced data sets. The data manager is to be provided with either a list, a dictionary, or a numpy array. These are traverse in order to save unbalanced data in smaller individual data junks. This avoids excessive memory consumption as obs... |
d541f2778fb242ed8cac5ba4e25e7ea5af0a05dd33656e87be048a48976b784b | Python | 7,298 | 187 | """
Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
Produces the final customer-facing web_summary.
"""
from __future__ import division
from websummary import summarize
import json
import martian
import numpy as np
import h5py
import pandas as pd
import os
from plots.plotly_tools import PLOT_CONFIG_KWAR... |
28982088a1f11e3da24f9b83384c93ce9e56048b1a3cdccbd92fe485456ee7ca | Python | 7,303 | 229 | def load_dnn_data(args):
"""Load the DNN feature maps of the training and test images, and of the
ILSVRC-2012 test and validation images.
Parameters
----------
args : Namespace
Input arguments.
Returns
-------
X_train : float
Training images feature maps.
X_test : float
Test images feature maps.
X_ils... |
3a52a39514dd54482868e5ffa90c6630dc40f4670d2f691715a4f63c64d6b0d8 | Python | 7,306 | 258 | """Inspect ICA results and apply them.
Here we load the previously computed ICA solution and use several
visualizations interactively to determine which ICA components
encode blinks, horizontal eye movements, and cardiac artifacts.
For this, we will use the VEOG, HEOG, and ECG channels in the data
to inform these deci... |
ee70f41f5b6ccb09f8b6ffd9b4cc5c4330b96a1aa44bbba26903b4e4b183e431 | Python | 7,307 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
5ef94e8e95cead08e238a7bf3e9124753770139715d17e62d14eca5b73e6363c | Python | 7,308 | 163 | # 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... |
9c5410b8619c5ac3b0802191dff7851906ff609e99805ac140ddca6f029646a1 | Python | 7,311 | 200 | from __future__ import annotations
import sys
from datetime import datetime
from functools import partial
from importlib import metadata
from pathlib import Path
from typing import TYPE_CHECKING
import scverse_doc.config
from docutils import nodes
from scverse_doc.registry import intersphinx
if TYPE_CHECKING:
fr... |
9abf2e542c06858ed4ba266d8b27dbeae68a5c77ba69d4e18dccc59f61b14dbd | Python | 7,312 | 224 | import matplotlib.pyplot as plt
from pylab import *
import numpy as np
import random
import math
import time
import os
import glob
# change the default font family
plt.rcParams.update({'font.family':'Arial'})
plot_in_tiff = True
def rmsd(x,y):
Nx = len(x)
Ny = len(y)
if Nx!=Ny:
print('WARNING! Nx... |
b2d57243f58d92f69ffc5e9b7189ca9a300c50407e95e2814904c204990a537e | Python | 7,314 | 189 | from spikingjelly.logger import logger
import multiprocessing
import shutil
from concurrent.futures import ThreadPoolExecutor
from pathlib import Path
from typing import Callable, Optional, Tuple
from torchvision.datasets.utils import extract_archive
from . import utils
from .base import NeuromorphicDatasetFolder
__... |
c3e2caeea94cb10d981db65140ff7926fa8cda01c649ee326198bb0973648ff3 | Python | 7,316 | 220 | """
Local Community Detection Algorithms
Local Community Detection (LCD) aims to detected one or a few communities
starting from certain source nodes in the network. This differs from Global
Community Detection (GCD), which aims to partition an entire network into
communities.
LCD is often useful when only a portion ... |
d4b07afdd8566abb84aae4283080774afdf8ed43e5a39917b5dd34f405bf19d8 | Python | 7,316 | 222 | """
Compiler for the intermediate representation of a Datalog program.
The :class:`DatalogProgram` class processes the
intermediate representation of a program and extracts
the extensional, intentional, and builtin
sets and has support for constraints.
"""
from typing import Iterable
from .expression_processing impor... |
8d2a4f6ce2f7241aace5d0c991a1714e16c7215ac7f2ac5da45f8189e4ee8f6f | Python | 7,318 | 173 | import numpy as np
import pickle
import torch
from torch.utils import data
from torch.utils.data.dataset import TensorDataset
from torch.utils.data import DataLoader
from torch.nn.utils.rnn import pad_sequence
from sklearn.preprocessing import StandardScaler
torch.set_default_dtype(torch.float64)
class MyDataset(da... |
09ac86f14bac60fd5c5519466736dd447280e7b6a8510f822df5ab0e1b7d0d69 | Python | 7,320 | 201 | # MIT License
#
# Copyright (c) 2019-2024 The PyQMC Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy,... |
855c139b550efdd46a026a6bfc8bbb2b22e9f1aab69c9f4aab55f2857d983876 | Python | 7,321 | 226 | import pathlib
import subprocess
from concurrent.futures import ProcessPoolExecutor, as_completed
import numpy as np
import pandas as pd
import pysam
import xarray as xr
import yaml
from ALLCools.mcds.utilities import write_ordered_chunks
from ALLCools.utilities import genome_region_chunks
from .rms_test import (
... |
bb79c09bf6a2017eb933b1edca52aead45dee422b74256a7589e54b12e3fe5e9 | Python | 7,322 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
b8e19682523df4616fcc35ae61bf09301b222303815503eda9bf4d4ee658707e | Python | 7,326 | 225 | import numpy as np
import random
import os
import sys
sys.path.append("../")
import pyedflib
from constants import INCLUDED_CHANNELS, FREQUENCY, ALL_LABEL_DICT
from scipy.fftpack import fft
from scipy.signal import resample, correlate
def computeFFT(signals, n):
"""
Args:
signals: EEG signals, (numbe... |
1abfee1c0928b288931337165d64375c6be20fdd9fb4983e4fa72f202ef00061 | Python | 7,331 | 194 | #### tests for scripts/run.py ####
# this is a long test, if want to exclude it for quick testing, run
# pytest -m "not slow"
# tested functionality:
# load_config, save_config
# overall training / evaluation functionality
# creation of expected folders when iterating over network or data parameters
# evaluatio... |
ff56b6087a49f991bb3794e0ffbdd6cde0fba7334ec622b42c99b6b5dd63d0a9 | Python | 7,331 | 277 | from typing import Literal, Optional
import torch
from torch.autograd.function import once_differentiable
from spikingjelly.activation_based import surrogate
from .. import surrogate_runtime as surrogate_objects
from ..native_loader import _native_available
from ..projection import (
_check_forward_inputs,
_... |
36bf2cce2aaafc339f99eb33f7b61e4cac68efa9ee38591d6c3971435cd776c4 | Python | 7,333 | 169 | from .strategy import Layered, PlacementStrategy
from ..helpers import assert_attr_array
import math, numpy as np
from ..exceptions import *
from ..reporting import report, warn
class Satellite(PlacementStrategy):
"""
Implementation of the placement of cells in layers as satellites of existing cells
Plac... |
bdb6f527ba41c353b0e86f6fe9adab2061a56bf9245b41f3d59a9e9cc93d703f | Python | 7,333 | 195 | import random
import time
import networkx as nx
import numpy as np
from gensim.models import Word2Vec
from cogdl.utils import alias_draw, alias_setup
from .. import BaseModel
class Node2vec(BaseModel):
r"""The node2vec model from the `"node2vec: Scalable feature learning for networks"
<http://dl.acm.org/cit... |
5b56c274364047d89623ec2557f39e363c85272e8200bb55e19192c7cf82de03 | Python | 7,334 | 108 | import os
import pandas as pd
import pathlib
from ..preprocess import base_dataset
from ..utils import helper_functions, check_functions
from ..model import _model_functions
def post_generate_feature_importances(results_directory_genotype_level: str, data_dir: str):
"""
Post-generate the feature importances... |
69d8b3bdff5a56a54c1fe27a3e4a41cc8d6e5c112036eb6437115a630d416489 | Python | 7,335 | 289 | from statistics import mean
import pandas as pd
import numpy as np
import glob
import os
import nilearn.signal
import matplotlib.pyplot as plt
from scipy import stats
import pingouin as pg
import seaborn as sns
from scipy.stats import bootstrap
#####################################
# arrg=np.array([[[[1],[2]],[[3],[4]... |
da8ee77ee23b062c0cccb52246119a6c6751f419d033a5c9619e170eec36247e | Python | 7,339 | 205 | from sqlalchemy import DDL
# function name prefix
fn_prefix = "fn_audit_history_by"
# channel used by pg_notify so HistoryAuditMonitor can LISTEN for updates
NOTIFY_CHANNEL = "galaxy_history_update"
# map between source table and associated incoming id field
trigger_config = {
"history_dataset_association": "his... |
3573e2ec064a219aafb53db2701006ab7e94babcbd60a8413a1764b6b80fd8f4 | Python | 7,340 | 245 | import tensorflow as tf
from tensorflow import keras
from keras import optimizers
from tensorflow.keras import layers
import numpy as np
np.set_printoptions(precision=5)
import matplotlib.pyplot as plt
import pandas as pd
pd.options.display.float_format = '{:,.5f}'.format
import scipy as sp
from scipy import stats
imp... |
93cd37d89e08b59e1a14778eada3a9885f32e1a3e6d8ed60e3852f51fad02608 | Python | 7,343 | 212 | """
Tests for the temporal aspect of the Temporal VF2 isomorphism algorithm.
"""
from datetime import date, datetime, timedelta
import networkx as nx
from networkx.algorithms import isomorphism as iso
def provide_g1_edgelist():
return [(0, 1), (0, 2), (1, 2), (2, 4), (1, 3), (3, 4), (4, 5)]
def put_same_time(... |
1118891efd7a6f9831649bff171b9fd80eca4b0ae9ec4cb1974dc24ea10a52db | Python | 7,348 | 225 | """The Möbius weights of inclusion-exclusion, computed with a containment
test that is not complete, see doc/inclusion_exclusion.rst.
"""
from fractions import Fraction
from random import Random
import pytest
from nl_expr.exceptions import NonLiftableException
from nl_expr.expressions import Symbol
from nl_expr.logic... |
c08e34d35ae1bb9e2f269bb88c71b5dfdf00852f659f7d2108c22454aa510135 | Python | 7,352 | 192 | #!/usr/bin/env python
# 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
# "L... |
975360bb3cfaf05bfdd459c04fbcbb0741974a88def6ea1688e6c7a3b4e58863 | Python | 7,354 | 268 | import pytest
from networkx.utils.mapped_queue import MappedQueue, _HeapElement
def test_HeapElement_gtlt():
bar = _HeapElement(1.1, "a")
foo = _HeapElement(1, "b")
assert foo < bar
assert bar > foo
assert foo < 1.1
assert 1 < bar
def test_HeapElement_gtlt_tied_priority():
bar = _HeapEl... |
7d08ad9e635032cbe0e2d140a35d4c2f2c528c758b0fac6f79b538ee8f5588b8 | Python | 7,355 | 234 | """Tests for the pretty-printer of named relational algebra plans."""
import operator
from typing import AbstractSet
from nl_expr.expressions import Constant, FunctionApplication, Symbol
from ...utils.relational_algebra_set import NamedRelationalAlgebraFrozenSet
from ..pretty_printer import PrettyPrinter, pretty_repr,... |
c4a1a339fb367cefe27b0f4cf56fa382afeb23fbafd41c956f4d7b99527c8163 | Python | 7,355 | 242 | import logging
import sys
from functools import partial
import numpy as np
import tqdm
from sklearn.base import (
BaseEstimator,
ClusterMixin,
TransformerMixin,
clone,
)
from sklearn.utils.validation import check_is_fitted
from divik.cluster._kmeans._core import KMeans
from divik.core import configura... |
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