sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
85063b38ae5b2e1dce44bbcdcf224d4c901dfcff4b0799480d52871aad576a99 | Python | 2,227 | 78 | # from torch.dataloaders.preprocessing import Dataset
# import torch
# import numpy as np
# import os
#
# from constants import DATA_DIR, BIN_LOCATIONS_DENSE, BIN_LOCATIONS
# class ROCFDatasetRegression(Dataset):
# """Face Landmarks dataset."""
#
# def __init__(self, df_metadata=None):
# """
# ... |
1ec16097e15460b7b8bd64a671aa11b8c697f26c4fb62242c7989e3254252565 | Python | 2,228 | 68 | from .bace import BACE
from .bbbp import BBBP
from .cep import CEP
from .clintox import ClinTox
from .delaney import Delaney
from .freesolv import FreeSolv
from .hiv import HIV
from .lipophilicity import Lipophilicity
from .malaria import Malaria
from .moses import MOSES
from .muv import MUV
from .opv import OPV
from .... |
68011293af6cd2cde11819e2caa9b56a63ebd7ca91410bc36baf22d0bc6cca13 | Python | 2,228 | 52 | """Regression: the custom-atlas hemisphere status must not raise NameError.
``_resolve_hemisphere_plane`` returns ``(plane, status_text)`` for the current
template. Its custom-atlas branch - reached when the user has DRAWN a midline on
a custom template and the run can read it back - built its status by appending ... |
e884935430145a9d00cf9c55e38fa5bee15c6f2f2de0be52ccd9a651d242334e | Python | 2,228 | 76 | from pathlib import Path
from typing import Any
import elasticai.creator.ir2verilog as ir
from elasticai.creator.file_generation import find_project_root as get_path_to_build
from elasticai.creator.ir import Registry, attribute
from elasticai.creator.ir2verilog import Ir2Verilog, factory
def _load_and_plugin(
ty... |
fdad7606953bef56af7f153f805eb531b49445826e3f5213febc9e74c292dd51 | Python | 2,228 | 43 | import numpy as np
import pandas as pd
import os
import sys
import subprocess
def do(cmd, get=False, show=True):
if get:
out = subprocess.Popen(cmd,stdout=subprocess.PIPE,shell=True).communicate()[0].decode()
if show:
print(out, end="")
return out
else:
return subpro... |
2ef15754613ff778170e49fa58ed6681ec65cfc77a1f70322371de3e437416dc | Python | 2,229 | 66 | from __future__ import division
import numpy as np
class DiscreteProcessEstimator(object):
""" This class estimates the emperical distribution of a discrete random variable over time. It forgets the
distribution with a user-specified time constant.
"""
def __init__(self, num_states, sample_rate,... |
49fdd088d051ad68fc771ef0760e4e2fafd462079bdaebcad4ae05e57a30bc28 | Python | 2,229 | 64 | import torch
import torch.distributed as dist
import torch.nn as nn
import torch.nn.functional as F
from collections import OrderedDict
class MLP(nn.Module):
def __init__(self, in_channels=1, out_channels=3, feature_channels=12, dropout_prob=0.2):
super().__init__()
self.in_channels = in... |
93f629ebe7d193347eb86849dddc0548fc26334444181677e1bff9b513ebaa3c | Python | 2,229 | 72 | import torch
from torch import nn
from typing import List, Optional, Dict
from .base import CutoffLayer, EmbeddingLayer
from ..utils import find_distances, _scatter_add, EnvPara
__all__ = [
"AtomicOneHot",
"AtomicNumber",
"AtomicEmbedding",
]
class AtomicOneHot(EmbeddingLayer):
def __init__(self, ele... |
b6877a484ce058dc46d329b6763e03f0790db2a0f12c70804336ecfcf3119f29 | Python | 2,229 | 52 | from scipy import linalg
from sklearn.covariance import EmpiricalCovariance,LedoitWolf
import numpy as np
def partial_corrconn(activity_matrix,estimator='EmpiricalCovariance', target_ts=None):
"""
activity_matrix: Activity matrix should be nodes X time
target_ts: Optional, used when only a s... |
016c6f38beae057ba0ef7e4b063e35a68d75b34de3d08d0fafa62b23d9a355d8 | Python | 2,230 | 52 | import read_files
import write_files
import data_handler
import offline_prep as prep
import online_use as use
import main_config as conf
import printer
if __name__ == '__main__':
# create files in results to save optimal parameters achieved by offline preparation
if conf.MODE == 'I':
write_files.init_... |
77dce424918a35a9bf3814c423b28d8f7f68494140ab0442784f2e7af87e2a43 | Python | 2,230 | 54 | #!/usr/bin/env python
import os
import pandas as pd
## location of main project directory on HPC
proj_path = '/project/3011157.03/Simon/proj_2022_CABB_movie/'
## location of R output files to visualize
r_path = os.path.join(proj_path, 'Scripts', 'MovVar_CommsBio_Revision01', 'control_length','r_output')
## location wh... |
8453fe0fd38c14fefdf42c2ee207ad643d8a74720ceaa6ff78e434e19aa81e84 | Python | 2,230 | 80 | import numpy as np
from .basic_euclidean import eucl_dist, eucl_dist_traj
from .basic_spherical import great_circle_distance
######################
# Euclidean Geometry #
######################
def e_erp(t0, t1, g):
"""
Usage
-----
The Edit distance with Real Penalty between trajectory t0 and t1.
... |
a1165531bc52a372d524c089eab88d292de577b380017e4f4ba886dced8dbb2f | Python | 2,230 | 82 | from __future__ import annotations
import pytest
from ase.atoms import Atoms
from quacc import get_settings
from quacc.calculators.mrcc import mrcc
from quacc.calculators.mrcc.mrcc import (
MRCC,
MrccProfile,
MrccTemplate,
_get_version_from_mrcc_header,
)
MRCC_EXECUTE = MrccTemplate.execute
def tes... |
bdbcc8cef41f83882788be7513d6c2102130697298b369dff9265b26489d7772 | Python | 2,230 | 51 | """Real-pair parity guard: matched ``affine`` split vs fused ``default``.
Guards the spec claim that ``--affine_method affine`` (explicit affine pass +
SyNOnly) reproduces the fused ``default`` path (``ants.registration(type_of_transform=...)``
unchanged) within ANTs run-to-run non-determinism. This is a real-data... |
0233ee2c3030e5b536e13213fa4094358b62033f075fcd301c255e1b497fe383 | Python | 2,231 | 50 | import os.path
import re
from collections import defaultdict
from ckg.graphdb_builder import builder_utils
def parser(databases_directory, download=True):
config = builder_utils.get_config(config_name="gwasCatalogConfig.yml", data_type='databases')
url = config['GWASCat_url']
entities_header = config['ent... |
cefabf97029abb5a49fac310b6cc1543aa0159eac17d25a5b578b52cead09ace | Python | 2,232 | 68 | """Run plotting
---------------
Create plots of the network activity of the mesocircuit.
"""
###############################################################################
# Import the necessary modules.
import os
import sys
import numpy as np
import h5py
import mesocircuit.mesocircuit_framework as mesoframe
import... |
50ab9cd1ed3742b2b20a8d6eca0406e21fc7943a0ef220f79df0b40162f06c87 | Python | 2,233 | 58 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from common_setup import IssueConfig, IssueExperiment, is_test_run
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["issue657-v2", "issue657-v3"]
CONFIGS = [
IssueConfig(heuris... |
e32695be3ce0baa7c6691014930e01d84125b7d866d754901ff1ca25eb150a9f | Python | 2,233 | 96 | # Node-group asset "LCh to OKLab" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING
... |
f521367ee91ac31f1d8729f69c321de1c273c50be42e2b6e43161a3fc93857f3 | Python | 2,233 | 58 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from common_setup import IssueConfig, IssueExperiment, is_test_run
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["issue657-v3", "issue657-v4"]
CONFIGS = [
IssueConfig(heuris... |
3fe52db7c86f30692425dc3b54fcd9d34ba28de03d76885408c4dc0db6de4245 | Python | 2,235 | 88 | import functools
import operator
import itertools
from .errors import OptionError
from .extern.jaraco.text import yield_lines
from .extern.jaraco.functools import pass_none
from ._importlib import metadata
from ._itertools import ensure_unique
from .extern.more_itertools import consume
def ensure_valid(ep):
"""
... |
33f3b70d5756c42e8a5d345d7144cd458d5f1a67d3021fb567b4f145ce993b77 | Python | 2,236 | 61 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# 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... |
897d2f81cd5a76e97aea4cb136906b73831403684df2cb17a95d42e84a8abb24 | Python | 2,236 | 70 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
90a19989ce9c260a37e92cd52a9322a615895f9c76cfd56924e0084a24257fc7 | Python | 2,236 | 53 | # ----------------------------------------------------------------------
# Copyright (C) 2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or mo... |
c1ad391d3527fd2f5c9601dcddf70610f5a95b0bdda44430765a999e73638bf6 | Python | 2,236 | 56 | # Copyright (c) 2020, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and t... |
ded51532c4c5e51970901e458b1230b51c5a0d964710023d2c0c4b2368c5fec0 | Python | 2,236 | 71 | from typing import Any, Callable
import elasticai.creator.ir as ir
from elasticai.creator.ir2vhdl import (
Instance,
LogicSignal,
LogicVectorSignal,
NullDefinedLogicSignal,
Signal,
)
from elasticai.creator.ir2vhdl import (
Node as VhdlNode,
)
from .node_factory import (
InstanceFactoryForC... |
44352ebcca8534b1fb20acf383211c8676947b33fecb8729c747ed85999df617 | Python | 2,237 | 54 | #!/usr/bin/env python
import os
import pandas as pd
## location of main project directory on HPC
proj_path = '/project/3011157.03/Simon/proj_2022_CABB_movie/'
## location of R output files to visualize
r_path = os.path.join(proj_path, 'Scripts', '04_2ndLev_ISRSA','r_output')
## location where visualizations and niftis... |
6aca20f0963612288606bf1b8d2cc7a2275a809bad0432302ebe35dd178fedfe | Python | 2,237 | 92 | import os
import sys
import numpy as np
import argparse
def check_actg(seq):
ret = ""
for x in range(len(seq)):
if seq[x] not in "ACTG":
ret = ret + seq[x]
return ret
def seq2kmer(seq, k):
kmer = [seq[x:x+k] for x in range(len(seq)+1-k)]
kmers = " ".join(kmer)
return kmers
... |
85512abae61e045b5f70eb4f7589d4b379f0bc7e180636c6e668d4a5e9b6d3b0 | Python | 2,237 | 71 | """Testing CLI command measure."""
import os
import subprocess
def test_measure():
"""Tests for morphometric mesurements."""
os.chdir(os.path.dirname(__file__) + '/data')
proc = subprocess.Popen(['swc', 'measure', 'pass_simple_branch.swc',
'-a', 'path', 'sholl'],
... |
8a9eff6f62d4e3427f2bbdef5bc81882baad61f87c0e4d0fe0a11dd981fb24de | Python | 2,238 | 62 | import math
import pytest
import smart
def test_Species_initialization(species_kwargs_A):
"""Test that we can initialize a SpeciesContainer"""
A = smart.model_assembly.Species(**species_kwargs_A)
assert A.name == species_kwargs_A["name"]
assert A.latex_name == species_kwargs_A["name"]
assert str... |
9c42e05fbedba4f8e6b24d932ff301817b709b2af5f936ae7069e880901e5c27 | Python | 2,238 | 56 | import os
import pandas as pd
from collections import defaultdict
from ckg.graphdb_builder import mapping as mp, builder_utils
def parser(databases_dir, download=True):
config = builder_utils.get_config(config_name="goaConfig.yml", data_type='databases')
url = config['url']
rel_header = config['header']
... |
2e30f04191898a5d7fbd7be105e48c8fd3e3fc7f58c26ebe3fa266acdccf347e | Python | 2,239 | 58 | import os
import tempfile
import unittest
import numpy as np
import torch
from torcheeg import transforms
from torcheeg.datasets import DEAPDataset
from torcheeg.io import EEGSignalIO
from torcheeg.models import FBMSNet, ViT
class TestInputValidation(unittest.TestCase):
def test_label_input_type_is_checked(self... |
e607cc1cd1f9d40a7bc0f02e75f2a0ae5013db51312528ead5e59543c6e41a67 | Python | 2,239 | 74 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# 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, modify, merge,... |
30efb26ca2d62cc8dbd651f9bc368bb0dc9713f8d6a98b18859303d9b5a6ee7e | Python | 2,240 | 61 | import os
import random
import unittest
import shutil
from torcheeg.io import MetaInfoIO
class TestMetaInfoIO(unittest.TestCase):
def setUp(self):
shutil.rmtree('./tmp_out/')
os.mkdir('./tmp_out/')
def test_init(self):
io_io_path = f'./tmp_out/{"".join(random.sample("zyxwvutsrqponmlk... |
3c22486f2bc298a5bc13401bcdd2d3d6bfbd79697c34e0abe932371c10ca1e51 | Python | 2,240 | 85 | import numpy as np
# registration
from pystackreg import StackReg
# parallel processing
from joblib import Parallel, delayed, parallel_backend
def get_tmats(arr, reg, n_bin=1):
"""Get transformation matrices for frames in array
Apply one of the methods in pystackreg.StackReg to align frames in array
to... |
fae93cb90bc5466104432ad669d6ceaa6b87a0912dfe96e961deb90fa32f9727 | Python | 2,240 | 70 | # flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2021 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
83deed7a06fc032f4e6c7d43c5178a0a49b39e0d3035d66edf0fdaa7ccdb5de6 | Python | 2,241 | 63 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from downward.experiment import FastDownwardExperiment
from downward.reports.compare import CompareConfigsReport
from relativescatter import RelativeScatterPlotReport
import common_setup
REPO = common_setup.get_repo_base()
REV_BASE = 'issue58... |
d34611e8de1757262ffbf64ebdbb16eb550101ab64c13b916a9ae6f55c19e982 | Python | 2,242 | 75 | #!/bin/env python3
"""
Example script: calculate phases and find phase defect lines (PDLs)
"""
import ithildin as ith
import numpy as np
import matplotlib.pyplot as plt
# plotting preparations: subplots in 2 rows and 2 cols
fig, ((ax00, ax01), (ax10, ax11)) = plt.subplots(2, 2, figsize=(11,9), dpi=360)
# load data
pr... |
39c6f110287136241004156edfecc65321ade8c5cc1733ddfd57f315d309cb07 | Python | 2,243 | 68 | """
Tests for CALIB module
FIXME need satrecov tests
FIXME need sensitivity correction tests
FIXME need test with edge correction
"""
import os
import pytest
import numpy as np
from fsl.data.image import Image
from oxasl import Workspace, reg, AslImage, brain
def get_wsp():
wsp = Workspace(debug=True)
wsp.... |
2ce4c295d426a8c588c6a6989475d3166b69d3aeeafd4ca711212f5015398f7b | Python | 2,244 | 66 | """
Bonito basecall
"""
import torch
import numpy as np
from functools import partial
from bonito.multiprocessing import process_map
from bonito.util import mean_qscore_from_qstring
from bonito.util import chunk, stitch, batchify, unbatchify, permute
def basecall(model, reads, beamsize=5, chunksize=0, overlap=0, ba... |
aa15502e642a1146d836297192a362d0dd47fe407092752e4b731323966f3033 | Python | 2,244 | 90 | # -*- coding: utf-8 -*-
#
# Top-level interfaces for the plotting functionality
#
from syncopy import __plt__
from syncopy.plotting.config import pltErrMsg
from syncopy.shared.errors import SPYWarning
__all__ = ["singlepanelplot", "multipanelplot"]
def singlepanelplot(data, **show_kwargs):
"""
Plot Syncopy... |
eb1c4b93cf050fa68eb2cab20b4430bf862ac2abb93a757a070e85075ddffe37 | Python | 2,244 | 76 | import torch
import torch.nn as nn
class Concater(nn.Module):
"""
Concatenates an output of some module with its input alongside some dimension.
Parameters
----------
module : nn.Module
Module.
dim : int, optional
Dimension to concatenate along. The default is -1.
"""
d... |
0a26dc8efe0a5ee0ad078ebccc3d06dac17d95ac45e367702503b1d837bcf6f8 | Python | 2,245 | 68 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
b1d15e4d870a944c4cd361d3eceb9cf55c41ba7e84ff8fbfabcb4c850e36b103 | Python | 2,245 | 74 | """Model wrappers.
Copyright (c) 2024 University of Michigan. All rights reserved.
Licensed under the MIT License. See LICENSE for license information.
"""
from typing import Dict, List
from itertools import chain
import torch
from torch import nn as nn
class MLP(nn.Module):
"""MLP for classification head.
... |
b95d9424d273b2f64b116dcd023f2ce0b031f9771d15b3d4a0c5058eefdabc91 | Python | 2,245 | 60 | """Tests for regtools.cell_counting_legacy.count_labels.
These are regression guards for the parameter-name fix in 95fbc31
plus basic shape coverage.
"""
import os
import pandas as pd
import pytest
class TestLoadSummaryStructures:
def test_reads_csv_via_filepath_param(self, tmp_path):
# The... |
cec3aed565e5d57e95b82b666a6105eca22709ea34331bb786a415311da5eddc | Python | 2,245 | 72 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
03c37aedd5d694a39a82b0bda59311213817f80deb74a62032b218d3092f0bbd | Python | 2,246 | 66 | # THIS FILE HAS BEEN AUTOGENERATED. To update:
# 1. modify the `_deps` dict in setup.py
# 2. run `make deps_table_update``
deps = {
"Pillow": "Pillow",
"black": "black>=20.8b1",
"cookiecutter": "cookiecutter==1.7.2",
"dataclasses": "dataclasses",
"datasets": "datasets",
"deepspeed": "deepspeed>0... |
c23ea3a49647a037815a0b826895221aecbbd328f46d83669e5e4e0f673d106c | Python | 2,246 | 57 | from cloudvolume import CloudVolume
import numpy as np
cv_path = "gs://neuroglancer/basil_v0/son_of_alignment/v3.04_normalized/split_masks"
def scale_slice(sl, dst_mip=1, src_mip=0):
scale = 2**(dst_mip - src_mip)
dst_sl = ()
for s in sl[0:2]:
dst_sl += (slice(s.start/scale, s.stop/scale), )
return dst_sl + (sl... |
6d0b73ac1cb3ef1e2843cc86c31d78c153003b5dfc0304d295de60481e0d09bc | Python | 2,248 | 50 | ###############################################################################
# This code generates the Supplementary Figure 7 of the paper "Longitudinal #
# single-subject neuroimaging study reveals effects of daily environmental, #
# physiological and lifestyle factors on functional brain connectivity" #
... |
4271c33db484350361fe4f2f8001643fca50f8c7afa33e13a7316b2d09d789e1 | Python | 2,249 | 54 | from pathlib import Path
import argparse
import dolfin as d
from smart import mesh_tools
import mito_parser_args
import numpy as np
def main(input_mesh_file, output_mesh_file, input_curv_file,
output_curv_file, num_refinements, single_compartment_im=False):
if not Path(input_mesh_file).is_file():
... |
49a06a8fd9c4aa344f549002cff34474f89e94184208594ce2ae8dcca92f734e | Python | 2,249 | 87 | # Node-group asset "Fallback Geometry" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHEC... |
3944d369156a3d62f05c501d55b4b883296848933608113c012ea1c4e79042ec | Python | 2,250 | 74 | import click
import pandas as pd
from prediction import max_value, weighted_mean
transformation = {
"maxvalue" : max_value,
"weightedmean" : weighted_mean
}
# options
@click.command()
@click.option('--predicted',
'predicted_tsv_file',
required=True,
type=c... |
8de313d86d64f8b3c8bcec9fb851fc20614d0505f01bca9770db49b1b138d082 | Python | 2,252 | 67 | from torch.utils.data import Dataset
import numpy as np
class DatasetNOE(Dataset):
def __init__(self, temp_data, noe_flag=False):
self.kssw_list = temp_data['ksw_1'].transpose()[:, 0]
self.fss_list = temp_data['fs_1'].transpose()[:, 0]
self.len = temp_data['ksw_1'].transpose().size
... |
92d71deafc2000654a588375939fee6da48bab467a9006f86101ce38c6e7cf23 | Python | 2,252 | 69 | import numpy as np
import pickle as pkl
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib as mpl
from matplotlib import rc
#rc('font',**{'family':'serif','serif':['Computer Modern Roman']})
## for Palatino and other serif fonts use:
#rc('font',**{'family':'serif','serif':['Palatino']})
font... |
bac9b1af0196fe3db4b0de793d0c549db277d5f294c34dc7426e296315356345 | Python | 2,252 | 74 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
6053118831b05cc76b0c41dcaf9d671868a6595742dd7d0751e32e4e31bfaafb | Python | 2,253 | 56 | from collections import defaultdict
#########################
# Diagnose entity - ICD #
#########################
def parser(ICDfile):
"""
Parses and extracts relevant data from ICD-10 files (Classification of Diseases).
:param ICDfile: list of files downloaded from the ontology database and used to gene... |
78ee29fc8c3556cf346d0bb99767e5a8219267e98c34c5111230d2b6af907e58 | Python | 2,253 | 57 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation... |
7b1bcbd1e3b4110e62cac7a682c5536e2e66a00544e4e5fe81083902e157cb04 | Python | 2,253 | 34 | import os
os.system("mkdir txtfiles")
#os.system("mv *txt txtfiles/")
for i in range(1,34):
os.system(f"mkdir txtfiles/C{i}")
os.system(f"cp patients/C{i}/plots/*.txt txtfiles/C{i}/")
os.system(f"mmv -d 'txtfiles/C{i}/avg_vel_grey matter_*' txtfiles/C{i}/avg_vel_grey_matter_#1")
os.system(f"mmv -d 't... |
04fa4950a2187dd625cf748bfad147873e337e8f3222b0a97a009f657ed17222 | Python | 2,254 | 60 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# 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, modify, merge,... |
d59f72e22f8197f857746eaef9a476ce85b03820663297b62653fa9ce49e5fde | Python | 2,255 | 71 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from lab.reports import Attribute, finite_sum
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.... |
168cafc60621049acdd0f6313d2f0baa138989ff5c2a94648e964ff656bd51ee | Python | 2,256 | 71 | from ECGPV_visualisation import *
import numpy
from matplotlib import pyplot as plt
from matplotlib.gridspec import GridSpec
a = ECGPV_visualisation(0.8)
ecgs = pickle.load(open('ecgs.pl', 'rb'), encoding='latin1')
def plot_ecg_to_specified_time(fig, ax, lead_name, t_end, counter):
ax.clear()
CL = 0.8
be... |
07b33378de18ce29e4751429d5cc6c81a9c7ccaa8d8f4476f05d4114bafae54c | Python | 2,257 | 54 | from ..region_1020 import (FRONTAL_REGION_LIST, GENERAL_REGION_LIST,
HEMISPHERE_REGION_LIST)
from ..standard_1020 import STANDARD_1020_CHANNEL_LOCATION_DICT
from ..utils import (format_adj_matrix_from_adj_list,
format_adj_matrix_from_standard,
format_... |
42b582dc6bf07121e9eda89df98c71dfb5edd5b2e087a0fc1cdf49c201405460 | Python | 2,257 | 90 | # -*- coding: utf-8 -*-
#from sys import argv
import numpy as np
from glob import iglob
import shutil
import os
import readline
from sys import argv
#def readfile(filename):
# f=open(filename)
# out=f.readline()
# f.close()
# print "read"
# except IOError:
# print 'File %s does not exist!' %/ (filename)... |
1cfd3f7e4026103a2ccfcadbbb9eddf51e376291ec8101c8d882a397e0797eb0 | Python | 2,258 | 86 | #!/usr/bin/env python3
## create personality distance matrix (correlation distance across 5 traits)
import os
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from sklearn.metrics import pairwise_distances
# ------------------------------------------------------------------
# paths
# --------... |
8d9b56c8740adfd004b0695e4403cf7fee79a41f34ac4f07693448300d7d81e6 | Python | 2,258 | 49 | from batchgenerators.utilities.file_and_folder_operations import *
import shutil
from nnunet.paths import nnUNet_raw_data
from nnunet.dataset_conversion.utils import generate_dataset_json
if __name__ == '__main__':
# this is the data folder from the kits21 github repository, see https://github.com/neheller... |
aecffe070cbdb7d6f2d782745a17789945f1cb91e5844f4457cd97c5109065f1 | Python | 2,258 | 85 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
c270fc2a5114d4ea185074d3ba5d9587ee07e896c218ba66701c174c9e458b6e | Python | 2,258 | 64 | from __future__ import annotations
import re
import urllib.parse
from wikibaseintegrator.datatypes.url import URL
from wikibaseintegrator.wbi_enums import WikibaseSnakType
class CommonsMedia(URL):
"""
Implements the Wikibase data type for Wikimedia commons media files
"""
DTYPE = 'commo... |
d653f99c0a24dab897d2ac54e68919dc741c2fbbca13f3990a65d3eded62b410 | Python | 2,258 | 70 | import numpy as np
import networkx as nx
def minkowski_dist(x, y, c=1):
"""Minkowski separation between x and y, c = speed of light parameter"""
d0 = -c**2 * (x[0] - y[0])**2
d1 = np.sum((x[1:] - y[1:])**2)
return d0 + d1
def minkowski_interval(N, D):
""" Sample N points from minkowski interval [a... |
e7a47f31155d6e9e0fa4084a07c0938288d2366f47aba3a9601535ae9a1bdc20 | Python | 2,258 | 76 | from typing import Dict, List, Optional, Callable
from ..base_transform import LabelTransform
class Multilabel(LabelTransform):
r'''
Apply multiple label transforms independently and combine their results into a list.
.. code-block:: python
from torcheeg import transforms
t = transfo... |
6487d10c094a78d134298487dc9a71d53b06836bbed91b5a8bf269cc05298bb4 | Python | 2,259 | 55 | import subprocess
# trigger = 'pe'
# thresholds = [4.3e-1]
# alfa = [2e-2] # for PE
# lmda = [5e0] # for PE
# trigger = 'always'
# thresholds = [1e-1] # just as a placeholder
# alfa = [1e-1] # for always
# lmda = [5e5] # for always
trigger = 'uncertainty'
thresholds = [2.5e-3]
# thresholds = [5e-4, 1.0e-3, 2.0e... |
aa3b21337831ab0da1a43ff0265cc18bb80ea85cded7a6ae3628b0cbfdb12c75 | Python | 2,259 | 55 | """
WikibaseIntegrator implementation of backoff python library.
"""
import logging
import sys
from functools import partial
from json import JSONDecodeError
import backoff
import requests
from wikibaseintegrator.wbi_config import config
log = logging.getLogger(__name__)
# Keyword arguments that may hold credential... |
ca735fbdf3ca9932add78a7bacdb40ade0c8f8cdbda0063208cb3812c04df763 | Python | 2,259 | 45 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
f58b87c5d25c2c00f7a2cbfe39621e0d01e597cf9ac21acfe7b4457172821f2e | Python | 2,260 | 62 | import numpy as np
from scipy.stats import gamma, norm
import sys
sys.path.append("../../lib_c/")
from state_estimation import smc_c
import matplotlib.pyplot as plt
import sys
sys.path.append("../useful_functions/")
import useful_functions as uf
def get_smoothing_trajectory(actions, rewards, idx_blocks, choices, subj_... |
4e7fa833dbe908bf07ff9c7d125a1415136658a254737b7e085f364656956b19 | Python | 2,261 | 68 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
a13ed0aef14d375aaf1d6298467fa2be6ee0b41bd74d6ed40e3aabff16aa02e3 | Python | 2,261 | 71 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from lab.reports import Attribute, finite_sum
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.... |
c6fc5eff4f3ed87bb0182cec7b6cffa28e82d79d51c54a16966e4c3fe717dfec | Python | 2,261 | 56 | """This example shows how to define the gradient of your own functions.
This can be useful for speed, numerical stability, or in cases where
your code depends on external library calls."""
import autograd.numpy as np
import autograd.numpy.random as npr
from autograd import grad
from autograd.extend import defvjp, prim... |
d1617fd1bf12ddfd640f7b055205c65ccef1f924e643e6c4ccd1b8a07f8464af | Python | 2,261 | 85 | import torch
import torch.nn as nn
import torch.nn.functional as F
from rocf_scoring.config import CONV_LAYERS, DROPOUT_MC_RATE, DROPOUT_MC
from rocf_scoring.data_preprocessing.loading_data import preprocess_dataset
from rocf_scoring.data_preprocessing.preprocess import BIN_LOCATIONS
import numpy as np
class CNN(nn.Mo... |
fcf41a3e808dd579b46d279e1d891c4263cdbd064ca577e1187671fb1cabde07 | Python | 2,261 | 89 | import socket
import globals.global_func as gf
def to_bytes(seq):
"""convert a sequence to a bytes type"""
if isinstance(seq, bytes):
return seq
elif isinstance(seq, bytearray):
return bytes(seq)
else:
return bytes(bytearray(seq))
class SocketException(OSError... |
1e426925df0521969658a354d42ddcf85103b53784591b8e9201374b88ffdf0c | Python | 2,262 | 98 | #!/usr/bin/env python
# coding: utf-8
# In[8]:
from pyteomics import mgf, mzxml, auxiliary
import numpy as np
import pandas as pd
# In[30]:
def input_from_mgf(path):
# Load the MGF file into a Pyteomics "MGF" object
mgf_file = mgf.MGF(path)
# Create an empty list to store the MS2 spectra
ms2_spec... |
51121c5fffd4b8085a13696ebb1d4fa9ba4d8dcb928a4f181c440b25632b4d13 | Python | 2,262 | 71 | #!/usr/bin/env python
# Copyright (c) 2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides an example control for pedestrians
"""
import math
import carla
from srunner.scenariomanager.actorcontrols.bas... |
be1a38a4cc653308ca4c2c09a4880364c725ae29017fd1bfc9fb96ed25de6075 | Python | 2,263 | 75 | # \file TestNiftyReg.py
# \brief Class containing unit tests for module Stack
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date May 2016
# Import libraries
import SimpleITK as sitk
import numpy as np
import unittest
import sys
import os
import pysitk.python_helper as ph
import pysitk.simple_itk_help... |
4fab779da39901fa30bd6800ef6258a47ec51103e09cd0b30f16e8d7fd40557e | Python | 2,264 | 70 | from typing import Optional, Union, Any
import torch
if torch.distributed.is_available():
from torch.distributed import group, ReduceOp
def distributed_available() -> bool:
"""
From pytorch lightning
"""
return torch.distributed.is_available() and torch.distributed.is_initialized()
def sync_dd... |
7814abd8e15fd79e85752faaf4dd1a0cb78a9601d42db1d887dc67e9db5aa76a | Python | 2,264 | 85 | from typing import Callable
import torch
import torch.nn.functional as F
def cos_sim(
x1: torch.Tensor,
x2: torch.Tensor
) -> torch.Tensor:
"""
Calculates similarity matrix based on the cosine similarity measure
Parameters
----------
:param x1: torch.Tensor
First input.
... |
15ff70980429b825612f183953f83f5ee0614677b532282e305ced094a0f2b8c | Python | 2,265 | 74 | from src.data_analysis.item import Item
from src.data_analysis.constants import *
class Assessment:
def __init__(self, assessment_id: int, fn: str, cheater_score):
self.__items = {}
self.__id = assessment_id
self.__filename = fn
self.__person = None
self.__inconsistent_row... |
5481d5fdf0d6491616f9804e2e342380486d0d23c6f6e76ded64c4931a42e2fa | Python | 2,265 | 93 | #
# Central pytest configuration
#
# Copyright © 2020-2025 Ernst Strüngmann Institute (ESI) for Neuroscience
# in Cooperation with Max Planck Society
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
# Builtin/3rd party package imports
import sys
... |
0c70e252eefc0da6f3dc2f7f7afa8f9f43897bbebb30cf814b2f00711d382fc7 | Python | 2,266 | 83 | """3D turbo spin echo sequence."""
# %%
import logging
import matplotlib.pyplot as plt
import numpy as np
import console
from console.interfaces.acquisition_data import AcquisitionData
from console.interfaces.acquisition_parameter import Dimensions
from console.spcm_control.acquisition_control import AcquisitionContr... |
16f3172530049bacbce5ee9658487b81907a26185fe497bb062e9fc8600b963c | Python | 2,266 | 45 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
e2505c037a759e024ed0a2e3522f9c17f777cec6a084ce4cfc55310ab24d0406 | Python | 2,266 | 73 | # === SOURCE CODE cfd-score-calculator.py provided by John Doench =====
import pickle, re
from os.path import basename, join, splitext, isfile, dirname
def get_mm_pam_scores():
"""
"""
# dataDir = join(dirname(__file__), 'CFD_Scoring')
dataDir='CFD/'
mm_scores = pickle.load(open(join(dataDir, 'mism... |
2ed1c71105715280521526ce6f0466c6d88b70f48f2fcce46f16c84eaa9e8f79 | Python | 2,267 | 52 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Found... |
5dfbaecdba94ce536005a60fdd855c3123026c64b1b552a5dd2567e49c722d35 | Python | 2,267 | 95 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 15 14:34:49 2024
@author: felipe
"""
import os
import sys
sys.path.append(os.path.abspath('../'))
from multiprocessing import Lock
from model.KuramotoControlled import Kuramoto
import concurrent.futures
import itertools
import gc
import numpy as n... |
2aaecdf2f077ab3ee74ca046fa0258694eb4de043f4947c74a3a2e2b14a77556 | Python | 2,268 | 72 | #!/usr/bin/env python
import argparse
from pathlib import Path
import skimage.io
from tqdm import tqdm
def main():
parser = argparse.ArgumentParser()
parser.add_argument('dir', help='root path of CTC dataset')
parser.add_argument(
'--3d',
dest='is_3d',
action='store_true',
... |
41f2bb287697acfe17d2b0b69358eb22960cea64508828ecd83fa164336ed59e | Python | 2,268 | 72 | import argparse
from concurrent.futures import ThreadPoolExecutor
from utils.api import get_filters_result_from_project
from dataset import TCGA_Project_Dataset, TCGA_Program_Dataset
from utils.logger import setup_logging
from pathlib import Path
from utils import set_random_seed
SEED = 1126
set_random_seed(SEED)
PRO... |
c742bbe083933cc4741313ac8ef20a179fd30d6e2734f3a63c07c41ae9180da3 | Python | 2,268 | 80 | from collections.abc import Iterable
from datetime import datetime
from elasticai.creator.file_generation.resource_utils import read_text
from elasticai.creator.hdl_ir import DataGraph
from elasticai.creator.ir2verilog import (
Code,
Registry,
TemplateDirector,
type_handler_iterable,
)
@type_handler_... |
0182e42a028bcd8ecd744680daf4ba714843845e70004349a1a94de124db3fef | Python | 2,269 | 86 | import numpy as np
from skfeature.utility.mutual_information import su_calculation
def merit_calculation(X, y):
"""
This function calculates the merit of X given class labels y, where
merits = (k * rcf)/sqrt(k+k*(k-1)*rff)
rcf = (1/k)*sum(su(fi,y)) for all fi in X
rff = (1/(k*(k-1)))*sum(su(fi,fj)... |
e89e54cfa582443e6da4143148d0b506df8997c956f58aa46f9cdb239430d205 | Python | 2,269 | 103 | from pytest import approx, raises
from wonambi import Dataset
from wonambi.detect.spindle import DetectSpindle
from .paths import psg_file
d = Dataset(psg_file)
data = d.read_data(chan=('EEG Fpz-Cz', 'EEG Pz-Oz'), begtime=35790, endtime=35820)
def test_detect_spindle_Moelle2011():
detsp = DetectSpindle()
a... |
13ea2ce71fd201cc975125269a52c9e2119422cc7368b8cfa6fb3efa8f8b68fa | Python | 2,270 | 54 | # -*- coding: utf-8 -*-
################################################################################
## *
## * Function: merge output p values fron replicates of GSEA]
## * Author: Siyuan Feng
## * Mail: siyuanfeng.bioinfo@gmail.com
## * Created: 04.19.2022
## * Last modified: 10.03.2022
################... |
600fa6c52a072fd0a5a2b5836bed8d22209726b22f95edc3d4c54dc2e974a841 | Python | 2,270 | 74 | import gzip
import json
from typing import List
from chemdataextractor.doc import Paragraph, Sentence
from pandas._typing import FilePath
from tqdm import tqdm
"""
1. CDE requires `python3.8`, best to start with a new venv.
2. CDE auto download bert models when first run
"""
def json_dump(filename, obj, gz=False, i... |
741e7f073a70e0039cc50e21c15622b43daf81df525b0a913e9e6cff4c68bb25 | Python | 2,270 | 76 | import matplotlib.pyplot as plt
import numpy as np
from PIL import Image
import cv2
from aug_utils import random_augmentation
from random import randint
def plot_figures(names, figures, nrows = 1, ncols=1):
"""Plot a dictionary of figures.
Parameters
----------
figures : <title, figure> dictionary
... |
7188848e131e7a47dafb29f4003c94d61fdacf2b7df9aa19e29d5e79c08dd60c | Python | 2,271 | 78 | from numpy import isnan
from wonambi import Dataset
from wonambi.dataset import _count_openephys_sessions
from wonambi.ioeeg import openephys
from wonambi.ioeeg.openephys import OpenEphys
from .paths import openephys_dir as filename
openephys.IGNORE_EVENTS = []
def test_openephys_count_sessions():
assert _coun... |
333f2e43e17d076758e73be2ef69c44d2340626a03a6eafc82d711ff8771fb13 | Python | 2,272 | 77 | #@ Context context
from java.io import File
from org.mastodon.mamut import WindowManager
from org.mastodon.mamut.project import MamutProject
from org.mastodon.tracking.mamut.trackmate import TrackMate
from org.mastodon.tracking.mamut.trackmate import Settings
from org.mastodon.tracking.mamut.detection import DoGDetec... |
5b5c91f02debe60004ac714c9f0511b53a062bdf372a513a97045f1a9db3ed89 | Python | 2,273 | 73 | # coding: utf-8
__author__ = 'ZFTurbo: https://kaggle.com/zfturbo'
if __name__ == '__main__':
import sys
import os
# For this test, make sure that only the tested framework is available
sys.modules['jax'] = None
sys.modules['torch'] = None
gpu_use = 0
print(f"GPU use: {gpu_use}")
os.... |
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