sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f54a59a85976432fdb295002f3b43c88df9f0bf5caaa868f08c065db8dee33ac | Python | 1,215 | 38 | """
Reads one or more fasta files, counts the number of amino acids of each type in the file.
"""
import argparse
import sys
import numpy as np
from esmologs import utils
from esmologs import __version__
import warnings
ALPHABET="ACDEFGHIKLMNPQRSTVWY"
CHAR_TO_IDX = {ALPHABET[i]:i for i in range(len(ALPHABET))}
... |
955e44a69ac61c089a0db531dadc909e955104660ffdaaa4b3e15af4fc3d1759 | Python | 1,218 | 41 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master... |
039c2b0824d9332daa21ba755534590669286ac0ed5fc07b7da6d6777f6a6c16 | Python | 1,220 | 38 | import numpy as np
import pytest
from pandas.errors import DtypeWarning
import pandas._testing as tm
from pandas.core.arrays import ArrowExtensionArray
from pandas.io.parsers.c_parser_wrapper import _concatenate_chunks
def test_concatenate_chunks_pyarrow():
# GH#51876
pa = pytest.importorskip("pyarrow")
... |
424d7b57c0133703a1f55fcbb98fba288a4b95648663448e2c03e78fcac89906 | Python | 1,220 | 39 | """
Example for how to load data and display results on one subject's cortical surface.
"""
import matplotlib.pyplot as plt
import numpy as np
import utils
import os
from scipy.stats import zscore
# Get path to data files
fdir = os.path.abspath('../')
modality = "listening"
subject = "01"
# Load training data for... |
bdd9ceb559d9c03f2c9bb3788d7112545508fe2d9324702119ec92354fd9d36b | Python | 1,220 | 45 | # libraries
import sys
import numpy as np
import pandas as pd
import samap
import scanpy as sc
import samalg
from samap.mapping import SAMAP
from samap.utils import save_samap, load_samap
# output
out_fn = "results_alignment_samap/"
# list of pairwise species comparisons
com_list = [ ["Xboc","Spur"], ["Xboc","Hmia"],... |
0a11b3f64f5899b679cd6bca521a6aa9fa2a1fef62e997c8b1246ac22400795c | Python | 1,221 | 48 | # JN 2015-01-09
"""
create a new folder for sorting
"""
from __future__ import print_function, division, absolute_import
import logging
logger = logging.getLogger(__name__)
import os
import numpy as np
import tables
def _set_attrs(h5file, attrs):
"""
helper
"""
for key, val in attrs.items():
... |
8688b9f82c179344e0929e6b19fcee45c7914cb605a5a0f760a66b2f1a9c5227 | Python | 1,221 | 34 | import sys
import re
def getFn( c, w ):
c = re.sub('(-l.|-[mnstuw]t?[0-9]+r?|-yQ)','',c)
s = c + ':' + w.lower()
expr = re.sub( '-x.*:', ':', s )
for xrule in re.split( '-x', c )[1:] :
## If morphological macro...
# (none yet)
## If 2-variable compositional lex rule, apply...
m = re.search( '(.... |
cb42002bcc6f1c498975641f6842e98fb1e0d77bacbd2cdd911104f17c9eab64 | Python | 1,222 | 35 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
b795966f30ee63797a5e6e0b40d8fa2ba4db582584962e5a3d5b94ee98ef9bc5 | Python | 1,226 | 32 | import pytest
import pandas as pd
import pandas._testing as tm
class TestDropLevel:
def test_droplevel(self, frame_or_series):
# GH#20342
cols = pd.MultiIndex.from_tuples(
[("c", "e"), ("d", "f")], names=["level_1", "level_2"]
)
mi = pd.MultiIndex.from_tuples([(1, 2), ... |
ede17f4de9e77a842bbad80d1da6cc5c91f4ba0761446234ec0968e2928f9e02 | Python | 1,228 | 39 | """
.. module:: cmd_volume
:platform: Linux, Windows
:synopsis: Command class for updating volume data via CmdManager
.. moduleauthor:: Fredrik Nysjo
"""
import gfx_utils
import numpy as np
class UpdateVolumeCmd:
def __init__(self, volume_, subimage_, offset_, texture_=0):
self.volume = volume_
... |
923c374285d730beecfe61b74f127bd35639143d6b7c6c931c925394aa957709 | Python | 1,231 | 42 | import warnings
import pytest
from pandas.util._exceptions import rewrite_warning
import pandas._testing as tm
@pytest.mark.parametrize(
"target_category, target_message, hit",
[
(FutureWarning, "Target message", True),
(FutureWarning, "Target", True),
(FutureWarning, "get mess", Tr... |
0636a749932b233ee1111295c144ae37e968689be52241eafe5f7796318ac031 | Python | 1,232 | 20 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
2694734e1c42c6c1ad5aeaadd5e0a3f2d40d4678e36886b13f03e153da675204 | Python | 1,232 | 31 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
ae5cf56072c5fba0a42932a607f771426a614499d30bca7159772773cabfb5ef | Python | 1,232 | 40 | import logging
from datetime import datetime
import pandas as pd
from Bio import SeqIO
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
def load_sequence_and_metadata(kind="csv"):
"""
Returns the sequences as a list of SeqRecords, and metadata as a pandas
DataFrame.
"""
startti... |
efeffc94d0a9462e6761bebc577a2f1f85dbd6de301380a38b942e7f78bd9aef | Python | 1,232 | 54 | """Create a string to parametrise condor jobs and print to terminal."""
from itertools import product
import os
from pathlib import Path
cwd = os.getcwd()
log_dir = Path(cwd) / 'logs'
log_dir.mkdir(exist_ok=True)
env = 'julearn'
exec_string = \
"1_predict_gf.py $(sign_threshold) $(corr_sign) $(cv)"
PREAMBLE = ... |
557d0e56128796d3e5488ad97ac79ea2fe55715d0296d8a49e533a6f2347036c | Python | 1,235 | 43 | # -*- coding: utf-8 -*-
import numpy as np
from .red_blue import RedBlueMove
try:
from scipy.stats import gaussian_kde
except ImportError:
gaussian_kde = None
__all__ = ["KDEMove"]
class KDEMove(RedBlueMove):
"""A proposal using a KDE of the complementary ensemble
This is a simplified version of... |
a3983cb43d79df62a813a8667450788d43efd62dbd0fcfb03279e7262cea82a2 | Python | 1,235 | 41 | """
naive.py
Created June 1, 2021
Naïve method for extracting digital signal from lead image using "center of mass".
"""
from typing import Iterator, Optional, Tuple
import numpy as np
from ... import common
def findFirstLastNonZeroPixels(oneDimImage: np.ndarray) ->Tuple[Optional[int], Optional[int]]:
def reve... |
c8eb435b3018f6dd06e6ae330a26c24d71bcb033938421ccfba4fd5992ed2dea | Python | 1,237 | 40 | # TODO get rid of this script and generalize
# resource-fmri/scripts/tile_stimuli.py to allow for different id_cols
import sys
import pandas as pd
import argparse
argparser = argparse.ArgumentParser('''
Tiles stimuli by subject and fROI into experiment data.
''')
argparser.add_argument('stimuli', help='Path to... |
67d10d39bbb64a007f126b41a30fe1d412b67e6060c8163e6b064b13f1aea4c3 | Python | 1,238 | 36 | #!/usr/bin/env python
import sys
from setuptools import setup
if sys.version_info < (3, 5):
raise NotImplementedError("Sorry, you need at least Python 3.5 to use tfserve.")
def readme():
with open("README.md") as f:
return f.read()
with open("requirements.txt") as f:
required = f.read().splitlin... |
9e59027d1547201fd198593f3392609a09550d9b5f342174bbdcc7aac44319e4 | Python | 1,238 | 42 | from datetime import datetime
import pandas as pd
import pandas._testing as tm
class TestInferObjects:
def test_infer_objects(self):
# GH#11221
df = pd.DataFrame(
{
"a": ["a", 1, 2, 3],
"b": ["b", 2.0, 3.0, 4.1],
"c": [
... |
f63356328e955561c179b375f5dfcc3360eaafa93d4e2bc7722d446f0db5f6d0 | Python | 1,238 | 26 | from GATF import prepare_dataloaders, get_model, train_epoch, test_epoch
import json
import torch
if __name__ == '__main__':
train_dataloader, test_dataloader = prepare_dataloaders(train_batch = 1024) # can be reduced to make the model fit smaller CPUs, performance might change.
with open("params/optimal_confi... |
9b794be0e765e443f8a9bdc301767b52949212571724b8087e0a94387acb1f96 | Python | 1,239 | 36 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
7cba16d61bb435c0613104ca7de26d4c20cc05210cce715c77b9be04d65d7778 | Python | 1,240 | 33 | """Goeminne et al. plasma-protein OrganAge models.
Original author code and coefficients:
https://github.com/ludgergoeminne/organAging
DOI: 10.1016/j.cmet.2024.10.005
The released coefficients are subject to the authors' Academic / Non-Commercial
License. Each converted artifact carries that license and its pinned pr... |
818d95074257a186011d0692aa6a14537929ff82733ff4d6a2b636a5f36d7d6d | Python | 1,243 | 34 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
9806f0d7542e24a6b35b131084df3809b5aa0529f13ae4565bcdba8bcc277c60 | Python | 1,243 | 24 | #!/usr/bin/env python
import os, sys
from Bio import SeqIO
def get_seqs_from_list(fafq, listfile, partial_ok=False, exclude=False):
f = sys.stdout
type = 'fastq' if fafq.upper().endswith('.FQ') or fafq.upper().endswith('.FASTQ') else 'fasta'
seqs = set([line.strip() for line in open(listfile)])
for r i... |
4678f2099ec3433e0c7cb26f68b877175594f88f57b5bf96b0b0ea461fa90a8d | Python | 1,245 | 52 | """nesvor entrypoints"""
import sys
import string
import logging
from .parsers import main_parser
def main() -> None:
parser, subparsers = main_parser()
# print help if no args are provided
if len(sys.argv) == 1:
parser.print_help(sys.stdout)
return
if len(sys.argv) == 2:
if ... |
9228fa048beb244a005f628fb476a0e31cf6e6c645bf3a2a662460373fe95328 | Python | 1,245 | 42 | import pandas as pd
# Parameters ---------------
annotations_file = './annotations_new_3s.csv' # Annotation file produced after running 'convert_avi_to_gif.py'
# Output CSV filenames for the training, validation and testing datasets
# that will be generated in this script
annotations_train = './annotations_train_3s.... |
cced40ef5504526a5ec205e65c67c6bb5b2ca4f5f65305373594314dc29fd658 | Python | 1,245 | 45 | """NotebookManager factory."""
from __future__ import annotations
import threading
from typing import TYPE_CHECKING
from pycaret_server.config import get_settings
if TYPE_CHECKING:
from pycaret_server.notebooks.base import NotebookManager
_lock = threading.Lock()
_singleton: "NotebookManager | None" = None
... |
1b24e1217ee4a2a02aef7489c1098b0289b626ab28fcd01e7f0095f61744374a | Python | 1,246 | 25 | # Detection of brain boundaries
from Environment import *
def remove_edge(image_path, label_array, critical_value=112, interval=15):
image = sitk.ReadImage(image_path)
image_array = sitk.GetArrayFromImage(image)
image_array[image_array > critical_value] = 255
image_array[image_array <= critical_value] = 0
binary_... |
e631130e42ca2d4806ec5d0a8eaf3686d1b9356bc2b983597f97f85f1b04eccd | Python | 1,246 | 39 | """Test the run_app CLI command argument parsing."""
import argparse
from lightning_pose.cli.commands.run_app import get_parser
class TestGetParser:
"""Test the get_parser function."""
def test_returns_argument_parser(self):
"""Returns an ArgumentParser instance."""
assert isinstance(get_pa... |
8ec763224054dbb80f273cc6ef72fad93d88d91194a6a81279aa6200c38343be | Python | 1,247 | 38 | import sys
'''
Convert itemmeasures to delim.lineitems, where each line is an space-delimited sentence, one per line, and article delimiter (!ARTICLE) are inserted between articles. Don't insert initial article delim, as it is inserted when converting later to linetoks.
'''
ARTICLEDELIM = "!ARTICLE"
docid = ""
sentid ... |
cdd0f7719c3933097a33928201b64991edeea90721058f6287a8a772a50680bc | Python | 1,247 | 40 | import sys, os
#from itertools import izip
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'resource-gcg', 'scripts'))
import tree
# File containing stripped linetrees
trees = open(sys.argv[1], 'r')
# File containing all words in Dundee corpus
words = open(sys.argv[2], 'r')
#curSent = word... |
176c546944843957e2e51faefb7a371eaa04e1f4693b956e2d5d84e4c0d89da4 | Python | 1,251 | 41 | """Plot heatmap visualization of worm pose in time."""
import numpy as np
import matplotlib.pyplot as plt
def heatmap(time, angles, clip=None, timestep=10, fig=None, ax=None):
"""Plot heatmap of pose data."""
xtimes = np.arange(min(time), max(time), timestep)
xticks = []
for i in xtimes:
ind... |
3642e015f55b4fef7caa996280a65ed822bc82419754e55b80b635adfedb0424 | Python | 1,252 | 30 | from Environment import *
from Parameter import *
# VISoR reconstruction of the generated BrainImage path with 561 channels and 488 channels to
# synthesize 3D images with (z, x, y) size (64,3500,2500)
def brain2dto3d(data_path, save_path, total_num, z_num, channel_index):
temp = []
j = 0
name_index =... |
c39a37ff92f0bc15bfd1797718abc93ef7b7edfd04b7ffa6de7a07eab2220def | Python | 1,252 | 33 | """Phase 2 object-storage abstraction.
Goal: stop hard-coding local-fs paths into the DB. Every artifact (Run
pickle, dataset snapshot, notebook output, registered-model bytes)
lands on an ``ObjectStore`` driver — same interface whether the bytes
live on disk, in S3, in MinIO, or in GCS/Azure Blob.
DB rows store **UR... |
8c9fb16e8c68cb44e2ec07a22b0967e7c58486c5b349ead86fb589647a6e8b38 | Python | 1,253 | 39 | # Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and relat... |
49c90ffa398fadf06a2dbce4607aa68bd440c19fc8e6cdbe34086c869c3818f3 | Python | 1,254 | 36 | import pytest
from src.pipeline import PipelineBuilder, PipelineRepresentation
from src.transform import SelectCols
from src.test_config import pipe_config
from sklearn.preprocessing import StandardScaler
import tempfile
import yaml
def test_pipeline_representation():
name = 'pipeline1'
description = 'Example ... |
007f010d3638c92634c4bbbefb141ba546cf575122999e1bcc7057948b8abe09 | Python | 1,255 | 32 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
a889037d6591257eaedb2f0eaf80908fd2a5f078d5e932ffd7e0bdcec6252fbc | Python | 1,255 | 42 | from __future__ import print_function
import pysam
import sys
inbam = sys.argv[1]
outbam = sys.argv[2]
readsin = pysam.AlignmentFile(inbam, "rb")
readsout = pysam.AlignmentFile(outbam, "wb", template=readsin)
last_reference = None
observed_reads = set()
for read in readsin:
reference_id = read.reference_id
... |
3740f1a352b5e6c5208d166c9d66e943666a28ef76449d06a33397a3dfd859ac | Python | 1,256 | 40 | import numpy as np
from numpy.random import default_rng
def get_population(min, max, N, seed=None):
"""get population between min and max with N samples
args:
min: minimum value
max: maximum value
N: number of samples
seed: seed for random number generator
returns:
... |
9aa5e466eefab76affe453b7295bd0952260bad9fbb037622eb5834bdf330e1f | Python | 1,258 | 30 | class SimArgs:
def __init__(self, n_in: int, n_delays: int, seed: int, r_mu: float,
r_std: float, tau_mem: float, noise_std: float,
nb_epochs: int):
# archi
self.n_in = n_in # number of input channels
self.n_out = 20
self.n_delays = n_delays # numb... |
4b4fbe6a8e68cc46aae3ccd8014b19c3e1ffdf31a766f268cfbdf77140dd9ae2 | Python | 1,259 | 38 | from VtkinterProcess.Vtkinter import Vtkinter
import threading
class VtkinterThread(threading.Thread):
def __init__(self, config=None, stimulator=None, threadName='Vtkinter', app='paint'):
threading.Thread.__init__(self)
self.name = threadName
self.config = config
... |
9cbe2efea126690f3fbe6eceac8d0eceb866e217f1a553e5ba91a0d07bbd4a4f | Python | 1,259 | 33 | import torch
class D2RLNet(torch.nn.Module):
def __init__(self, input_size,
units,
activations,
norm_func_name = None):
torch.nn.Module.__init__(self)
self.activations = torch.nn.ModuleList(activations)
self.linears = torch.nn.ModuleList([])
self.norm_layer... |
baa269b07049a69cec2080ea3ccbb106215d6ed1aa8c8e4fef18b3b7a4944b0b | Python | 1,259 | 40 | # -*- coding: utf-8 -*-
"""
Created on Wed Aug 26 20:08:08 2020
@author: KerschensteinerLab
"""
import pandas as pd
import numpy as np
from tkinter import filedialog, Tk
import os
from hunting_analysis_functions import *
#import cricket_hunting_analysis_dataframe as ck
#select h5 files and mp4 to analy... |
cad27b20c694f8505b6db3b65ece75187a463edb1f2e5f35888654526eb929bd | Python | 1,259 | 42 | import reverb
import tensorflow as tf
class VariableContainer:
def __init__(
self,
# ---
db_server: str,
# ---
table: str,
variables: dict,
):
self._table = table
self._variables = variables
# Initializes the reverb client
self.t... |
e0c35c4ecfd480685cc3f9c3acbf9c1936362b15fbb52ebd9334aaf0f009f643 | Python | 1,259 | 48 | import os
import pysam
# # NanomonSV's VCF format does not fit the truvari comparison, so we need refine its format
# # STEP 1: bcftools sort
# # STEP 2: SVINSLEN --> SVLEN
# # STEP 3: reformat GT
raw_vcf_path = "/mnt/d/workspace/svision-pro/paper_revision/real_nt_hcc1395/ont/nanomonsv.s2.vcf"
output_vcf_path =... |
12378dfa903f253f6704f5dadee2f28f1fbab7ba1eed82c0a46ff4283cf39c38 | Python | 1,260 | 41 | import numpy as np
import pytest
import pandas as pd
class TestCopy:
@pytest.mark.parametrize("attr", ["index", "columns"])
def test_copy_index_name_checking(self, float_frame, attr):
# don't want to be able to modify the index stored elsewhere after
# making a copy
ind = getattr(floa... |
fc32f6db44b2aaf4667111bd63a3286d5c1bb73299345bd959b267d7c0c72e9c | Python | 1,261 | 33 | """Tests for padding and cropping of data tensors."""
from typing import Literal
import pytest
import torch
from mrpro.utils import RandomGenerator
from mrpro.utils.pad_or_crop import pad_or_crop
@pytest.mark.parametrize('mode', ['constant', 'reflect', 'replicate', 'circular'])
def test_pad_or_crop_content(mode: Li... |
407ecb29916563ec8c7e520164f6c148bfb72e20a92484dac56db264a7a8dbcb | Python | 1,262 | 29 | from .files import import_data, save_data
from .wavenet import hidden_layer, normalize, generate_stepwise
from .ooc_compute import ooc_training
from .user_interface import set_config
from dask import array as da
import numpy as np
def training(param, euler_dict, model, var, **IC_train):
neurons = hidden_layer(par... |
2e290d029dc9f7045a2908c4db2292cf6f58941644b2eab02a37e04a5b0d93bf | Python | 1,263 | 40 | # -*- coding: utf-8 -*-
# Copyright (C) 2019 Andrea Vázquez Varela
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#... |
4c57d5d2c7f24876b67ced0f8990816b0a49eada8ad8971e3ab8c14987df06d9 | Python | 1,263 | 30 | # Production of training data
from Environment import *
from Parameter import *
def load_tif2array(file):
image = sitk.ReadImage(file)
image = sitk.Cast(image, sitk.sitkFloat32)
image_array = sitk.GetArrayFromImage(image)
image_array = np.transpose(image_array, [0, 2, 1])
return image_array
d... |
de1b3dcdb9f4efb2994d32b228d8b71248aa82d3271d570a798283463c20bb08 | Python | 1,263 | 41 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
dtlike_dtypes = [
np.dtype("timedelta64[ns]"),
np.dtype("datetime64[ns]"),
pd.DatetimeTZDtype("ns", "Asia/Tokyo"),
pd.PeriodDtype("ns"),
]
@pytest.mark.parametrize("ldtype", dtlike_dtypes)
@pytest.mark.parametrize("rdt... |
327c9c65a942bd6b4f84dc3c75a5d9d4261e43b65b4d48727de1ac1c108c7c16 | Python | 1,264 | 39 | from sys import path as sys_path
sys_path.append('..')
sys_path.append('../base')
import os
import matplotlib
if 'DISPLAY' in os.environ:
matplotlib.use('qt5Agg')
else:
matplotlib.use("Agg")
os.environ['CUDA_VISIBLE_DEVICES'] = '1'
from base.loggingUtils import setup_default_logging
from base.kernelFunctions i... |
9b44c32a39ad269ab79026724ff84b71221883981b408190bcef33026e42214e | Python | 1,265 | 26 | import models.args
import os
def get_args():
parser = models.args.get_args()
# Model arguments
parser.add_argument('--lr', type=float, default=0.00001)
parser.add_argument('--weight-decay', type=float, default=0)
parser.add_argument('--max-tokens', type=int, default=4096,
he... |
a052b2c7b200306e7ea719110074865e721f8b9374e94b98b74068a5d9a94bce | Python | 1,265 | 40 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
ca4e7f537a704ff3a35ed29992f67737c85c27777d1ac548b945be4d57def202 | Python | 1,266 | 44 | from numba import njit
from numba.types import bool_
import numpy as np
import torch
@njit("(int64[:], int32[:], int32)")
def remove_duplicates(spike_times, spike_clusters, dt=15):
'''Removes same-cluster spikes that occur within `dt` samples.'''
keep = np.zeros_like(spike_times, bool_)
cluster_t0 = {}
... |
fe2a9892bc355e8f05032446e1b2e45491a4a80c179a5d91f9c4e94e973372d0 | Python | 1,266 | 39 | import tensorflow as tf
class DuelingDQN(tf.keras.Model):
def __init__(self, action_space):
super(DuelingDQN, self).__init__()
self.fc1 = tf.keras.layers.Dense(
512,
activation="elu",
kernel_initializer=tf.keras.initializers.Orthogonal(tf.sqrt(2.0)),
)
... |
3425deac45f832890d8ec494ddedad5957a45ad0ae840cba18ba886ce38aeae0 | Python | 1,267 | 44 | import pytest
import pandas._testing as tm
from pandas.core.arrays import DatetimeArray
class TestAccumulator:
def test_accumulators_freq(self):
# GH#50297
arr = DatetimeArray._from_sequence(
[
"2000-01-01",
"2000-01-02",
"2000-01-03",
... |
16704276f252171d14e54778ae8d762a44c4162fab760d2220fc105e39ca0ba0 | Python | 1,268 | 43 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Function for making sensory motor ROI.
Created on Fri Jan 18 14:24:35 2019. @author: mikkel
"""
import mne
from surfer import Brain
# Make sensory-motor ROI based on aparc.a2009s
def make_sensorymotorROI(subj, subjects_dir, hemi='both'):
atlas = 'aparc.a2009s' ... |
2d483a71748cf024a5dd91f1187ddb33d3db90743bda94fb4d2f5b839e1fec16 | Python | 1,269 | 40 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
4ba2d2f4d14db100a941784576cf0b2e1e4b4b9237cedf7eb8c4ffd3a4856ae7 | Python | 1,271 | 36 | import pytest
import pandas as pd
import pandas._testing as tm
class TestSwaplevel:
def test_swaplevel(self, multiindex_dataframe_random_data):
frame = multiindex_dataframe_random_data
swapped = frame["A"].swaplevel()
swapped2 = frame["A"].swaplevel(0)
swapped3 = frame["A"].swapl... |
808d3b5ddc9f295213626037d43549573e4ea033e745e5c87d30e2b6e2b7eb23 | Python | 1,272 | 44 | """Class for Density Compensation Operator."""
import torch
from mrpro.data.DcfData import DcfData
from mrpro.operators.EinsumOp import EinsumOp
class DensityCompensationOp(EinsumOp):
"""Density Compensation Operator."""
def __init__(self, dcf: DcfData | torch.Tensor) -> None:
"""Initialize a Densi... |
b181dc97996c8fbc2eb750a21592b892719f798b047dbd7956cd68c817296527 | Python | 1,273 | 44 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 18 15:41:13 2021
@author: rishikesh
"""
import torch
import numpy as np
from torch import nn
def off_diagonal(x):
# return a flattened view of the off-diagonal elements of a square matrix
n, m = x.shape
assert n ... |
6da778b07310096f77914b7cd570410709fc08e2923539167d01a01a87d9cde8 | Python | 1,274 | 39 | import pandas as pd
def test_is_monotonic_increasing():
# GH#17717
p0 = pd.Period("2017-09-01")
p1 = pd.Period("2017-09-02")
p2 = pd.Period("2017-09-03")
idx_inc0 = pd.PeriodIndex([p0, p1, p2])
idx_inc1 = pd.PeriodIndex([p0, p1, p1])
idx_dec0 = pd.PeriodIndex([p2, p1, p0])
idx_dec1 = ... |
eb1588cbb25870eeb948051bc1a16fa0c0d961b35782e7d76bfdcccfe30c3ebe | Python | 1,274 | 45 | from OperationSystem.AnalysisProcess.TestingProcess import TestingProcess
from OperationSystem.AnalysisProcess.WaitAnalysisProcess import WaitAnalysisProcess
import json
class AnalysisController:
def __init__(self):
self.current_process = None
self.algorithm = None
self.actualWin = ... |
940a28a79fa8e3df59b7b8876b6d1f1cff42621f0d7825cda0f3bce71c6ca5f7 | Python | 1,275 | 31 | import sys, argparse
import pandas as pd
argparser = argparse.ArgumentParser(description='Generates geco.evmeasures data table.')
argparser.add_argument('f1', type=str, nargs=1, help='Path to experiment data table')
argparser.add_argument('f2', type=str, nargs=1, help='Path to itemmeasures data table')
args, unknown =... |
4f2e5b3389cbcf0c83bc5adad8f74d230bae61577f6ed3234010c761744fa827 | Python | 1,276 | 49 | import argparse
import h5py
import nibabel as nib
import numpy as np
import os
DIR = os.path.dirname(os.path.realpath(__file__))
print(DIR)
# %%
parser = argparse.ArgumentParser(description='convert .h5 to .nii')
parser.add_argument('--input_data',
default='meas_MID00402_FID02551_EPISeg2_67_1p0is... |
53d7af7ad96b25847d22b9bc73f0c5847a879061d274f759a3b9e8ce653c0ae8 | Python | 1,276 | 45 | import argparse
# Evaluates the dice score of segmentations given directories with saved
# segmentations in npy format.
def get_args():
parser = argparse.ArgumentParser(
description='Train UNet Model',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
'-c',... |
8a734643b88a93e7672de1065993b6ffcabdafd55b5000f1d792b4b9163c8f6f | Python | 1,277 | 65 | """
Data I/O API
"""
from pandas.io.clipboards import read_clipboard
from pandas.io.excel import (
ExcelFile,
ExcelWriter,
read_excel,
)
from pandas.io.feather_format import read_feather
from pandas.io.html import read_html
from pandas.io.iceberg import read_iceberg
from pandas.io.json import read_json
fro... |
97b0da873996fbf1fe0901d5c806d71e602184b06d8d7c37bdd8881602c9f3a5 | Python | 1,277 | 29 | # from initialization.config import *
# from initialization.initialization import *
#
# from data_processing.cell_identifier import *
# from data_processing.cleaning_formatting_filtering import *
# from data_processing.clustering import *
# from data_processing.data_io import *
# from data_processing.data_wrangling imp... |
ee88502bc18213ae8bea9302df658a5ce4e57ad981673f8baeca85f6a5327adb | Python | 1,277 | 49 | """Keep executable sources and user documentation on the current data host."""
import re
import subprocess
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
SOURCE_PATHS = (
"src",
"clocks",
"docs",
"tutorials",
".github",
"Makefile",
"pyproject.toml",
"uv.lock",
... |
b8659341177259783bebd8a0193c5fce8796f8a67b7b34775f9b226391a94d70 | Python | 1,278 | 29 | # from initialization.config import *
# from initialization.initialization import *
# from data_processing.cell_identifier import *
# from data_processing.cleaning_formatting_filtering import *
# from data_processing.clustering import *
# from data_processing.data_io import *
# from data_processing.data_wrangling impo... |
e202c230fdcd82e16dd338b796384675ba8d046bea2f76d8a99cf510b139f27a | Python | 1,278 | 25 | import tempfile
from esmologs import fasta2foldseek
import helpers
def test_fasta2foldseek_1(shared_datadir):
with tempfile.TemporaryDirectory() as output_dir:
#output_dir = "tmp"
fasta2foldseek.main(["--aa", str(shared_datadir / "af2_examples.pep.fasta"), "--tdi", str(shared_datadir / "af2_example... |
a3e5aa9bec24206f1fcf5490922d51a838c0b5bbd70716a1431d5fba0e8c2efa | Python | 1,279 | 47 | from datetime import (
UTC,
datetime,
)
import dateutil.parser
import dateutil.tz
from dateutil.tz import tzlocal
import numpy as np
import pandas as pd
import pandas._testing as tm
from pandas.tests.indexes.datetimes.test_timezones import FixedOffset
fixed_off = FixedOffset(-420, "-07:00")
class TestToPyD... |
5c779bb4bc949c3a12515b545bba394b0dc8b05035de70f1578610be10aa806e | Python | 1,281 | 38 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
196fc223c5d436d93397abe9a6a2dc8458440eb83cf3bf9353e48131611c70b7 | Python | 1,282 | 53 | import torch.nn as nn
class View(nn.Module):
def __init__(self, shape_out):
super(View, self).__init__()
self.shape_out = shape_out
def forward(self, x):
return x.view(self.shape_out)
class Permute(nn.Module):
def __init__(self, dims=(1, 0, 2)):
super(Permute, self).__in... |
047e51da5337e733517ffccc377f12eaccb75078f320cfdff11e5a6b8ae6aa56 | Python | 1,283 | 49 | #!/usr/bin/env python
'''
Testcases for the loiter detection
'''
import windseer.utils as utils
import windseer
import numpy as np
import os
import unittest
windseer_path = os.path.dirname(windseer.__file__)
testdata_folder = os.path.join(windseer_path, 'test', 'testdata')
test_file_hdf5 = os.path.join(testdata_fold... |
a72c03942c2c27eb67798924fcd483fb979c0c98ee3dfe52de54a3411c145e0c | Python | 1,285 | 36 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version
_env = 'ant'
_name = f'{_env}_{version}'
_iterations = 10000
_pbt_num_policies = 3
_params = ParamGrid([
('pbt.policy_idx', list(range(_pbt_num_policies))),
])
_... |
12324dc5d3f2ff4976fbb08eb4435ad3a196c2daa434045408391598c090a07d | Python | 1,286 | 36 | from msmfcode.core.logging import log
from msmfcode.core.config import *
from msmfcode.execution.parallel import ParallelExecutor, ParallelEvaluationExecutor
from msmfcode.models.cann import DMSMF, FMSMF, Grid, SSSF
from msmfcode.evaluation.plot import plot_weight_distribution, plot_neuron_activity_fixed_attractors, \
... |
126e9b36941cd69cbf60db518145b6955ce4a62ba6510bd256d34eff12e737a3 | Python | 1,286 | 55 | import numpy as np
import pickle
def get_griddata(griddata):
with open(griddata, 'rb') as f:
return pickle.load(f)
def get_grid(grid):
parameter = {}
with open(grid) as f:
for line in f:
data = line.strip().split()
parameter[data[0]] = np.array(data[1:], dtype='f... |
4a52a799ce7c2f6ab9014bdc0594b6032988b9dd4e704435b46a6506bc15282b | Python | 1,286 | 35 | from pathlib import Path
import pandas as pd
import numpy as np
class StatsFile():
def __init__(self, file: Path, type: str) -> None:
self.file = file
self.type = type
self.stats = pd.read_csv(file, sep='\t')
self.stats.rename(columns={'Measure:volume':'subject_id', 'lh.aparc.volume... |
32287049be422e96934d796e903e6a52d21dc7976feb298de979092b2e9f3923 | Python | 1,289 | 44 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
90ddb1f3e94cf4e9501670b9f9295fd6225b2ecf0b93cad75445c56320028853 | Python | 1,291 | 55 | # -*- coding: utf-8 -*-
"""
Created on Wed Jun 21 19:39:01 2023
Convolutional Spiking Neural Networks for Intent Detection Based on Anticipatory
Brain Potentials Using Electroencephalogram
Authors: Nathan Lutes, V. S. S. Nadendla, K. Krishnamurthy
"""
# train different networks on paper 1 using k fold cross-validati... |
4004ac91c4cb14f986793494ad7c6ecbb6ecc84be118e731b51dcd7fc8329e49 | Python | 1,293 | 47 | """Declarative base + reusable mixins.
Every table gets UUID v4 `id` + `created_at` / `updated_at`. Most get
`created_by` as an FK to `users.id` — that's added per-model rather than in a
mixin because the FK is awkward to express before `User` is defined.
"""
from __future__ import annotations
import uuid
from datet... |
6c59416be2af4c91b386a79c3fa54f831bb6af4b32fc6535f3e0926c208576df | Python | 1,293 | 34 | import sys, re
resources = {}
for path in sys.argv[1:]:
with open (path, 'rb') as f:
line = f.readline()
while line:
while line and not line.strip().startswith('define RESOURCE-DESCR'):
line = f.readline()
if line:
descr = ''
... |
8894809a1a4a3cf9e2e31c0be5222fac759725b5464bc155dc0520c655fec0aa | Python | 1,295 | 50 | import sys, os, argparse
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'resource-gcg', 'scripts'))
import tree
argparser = argparse.ArgumentParser('''
Prints a CoNLL style table of word and PoS tags from linetrees input.
''')
argparser.add_argument('-i', '--noindex', dest='i', action='store_true'... |
e31cdceb0d82eb0dc6bc275fbaa07e299a6d273fe32b217ee748fafe6bf71248 | Python | 1,295 | 28 | """
Some notes on how to extract e-fields from simnibs/pynibs FEMs at a cortical target.
This expects optimal coil placements computed with https://gitlab.gwdg.de/tms-localization/papers/tmsloc_proto
"""
import h5py
import pynibs
headmesh_msh = "path/to/simnibs/headmesh.msh" # original simnibs mesh
headmesh_hdf5 = "p... |
a91d275f86de1642167ee3fb85e2d675d56e6fb66799e6ceb63cb954d8c98d8f | Python | 1,297 | 32 | import sys, argparse
import pandas as pd
argparser = argparse.ArgumentParser(description='Generates provo.evmeasures data table.')
argparser.add_argument('f1', type=str, nargs=1, help='Path to experiment data table')
argparser.add_argument('f2', type=str, nargs=1, help='Path to itemmeasures data table')
args, unknown ... |
2a0390eafe86ce85d85ea447c9b24c23dc568636e20b705e086f874bc9c85cb2 | Python | 1,299 | 36 | """Test backbone factory."""
import pytest
from lightning_pose.models.backbones.factory import (
_build_convnet_backbone,
_build_transformer_backbone,
build_backbone,
)
class TestBuildBackbone:
"""Test the build_backbone function."""
def test_raises_for_unknown_backbone(self):
"""Raises... |
2cb430ac3e1d96caf44fb6c5ef29294d166a86e89a53e58a17fb165833f88835 | Python | 1,299 | 24 | """Model/training/evaluation/explainability pipeline (Phase 2b).
Ports the scientifically meaningful behavior of `Training.ipynb` and
`Heatmaps.ipynb` (see `docs/legacy-notebooks-inventory.md`) into current,
typed Python. **Imports TensorFlow unconditionally**; run `just install`
(installs the `model` extra along with... |
50be93f65d9739e9e71e05382f0763fa04a1d7da99a89939712f28aaaa2cc654 | Python | 1,299 | 43 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 agre... |
2274587ffd9af822e9acb29bfb9d681a5c382cda4c2f9b721a5679205d7539c0 | Python | 1,300 | 35 | import numpy as np
import pandas._testing as tm
class TestAutoCorr:
def test_autocorr(self, datetime_series):
# Just run the function
corr1 = datetime_series.autocorr()
# Now run it with the lag parameter
corr2 = datetime_series.autocorr(lag=1)
# corr() with lag needs Se... |
4a50be5e865d38f5c473d766e5d498f43b1f47d099556506b9491c198ca1b7ac | Python | 1,300 | 43 | import numpy as np, matplotlib.pyplot as plt, matplotlib.cm as cm
import pumpprobe as pp, wormdatamodel as wormdm
folder = "/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210907/pumpprobe_20210907_141336/"
fconn = pp.Fconn.from_file(folder)
signal = wormdm.signal.Signal.from_file(folder, "green")
ie = 15
time,t... |
878ff2ed523bad0ff56330a482288b5014f1c02da9b511262cf7ad6e16591a13 | Python | 1,301 | 32 | """Dictionary batches keep the worker/agent dimensions with one worker too."""
import numpy as np
import pytest
from rl_games.common.tr_helpers import dicts_to_dict_with_arrays
@pytest.mark.parametrize('workers', [1, 2, 4])
@pytest.mark.parametrize('add_batch_dim', [True, False])
def test_dictionary_collation_preser... |
f107912fb2d0b1d6617ddd6fb6785ebd67d3ba7b467f22eea51e61d84aae177a | Python | 1,301 | 46 |
import cine
from matplotlib import pyplot
import tube2
import keras
import numpy as np
from skimage import io
model = keras.models.load_model("meniscus_utils/meniscus_track_4")
FILENAME = "data2/unsuitableVideos/moth22_2022_02_04_Cine1.cine"
PAUSE = 0.5
#fig, ax = pyplot.subplots()
try:
video = cine.Cine(FILENAME... |
71fb31fe93bfcdc851ccd11bb1738646f4daeddf6877c4b9865f912d35a5b269 | Python | 1,302 | 33 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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 agre... |
84fb0cc3a0171d8dcebc2ef988b40b7f2bce09ee5ae7697b5231094ec9c4e665 | Python | 1,302 | 39 | # Copyright 2019 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
#
# http://w... |
f546b797637527c468ab380ded9fe2a18c88c020812de20a8557ab6d0222fec9 | Python | 1,302 | 35 | """Load digitclutter.
"""
import os
import pandas as pd
import numpy as np
import torch
from torch.utils import data
from PIL import Image
from torchvision import transforms
class Digitclutter(data.Dataset):
def __init__(self, path, root='./_data', transform=None, image_size=None):
if image_size is None:... |
7396714ada5d3e5db76202a7485fd4d4239be02687548d279ae4ed7b50d4a42d | Python | 1,303 | 66 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Created by Roberto Preste
import pytest
import os
from mtoolnote.tests.constants import (
HUMAN, HUMAN_ANN, HUMAN_ANN_CSV, HUMAN_ANN_HAPLOS, HUMAN_ANN_HAPLOS_CSV,
GGALLUS, GGALLUS_ANN, GGALLUS_ANN_CSV
)
@pytest.fixture
def human_vcf():
"""Open the human vcf... |
1c93b8d2d57839cd06873375e0c99142d15e81e6bc66ca126dac2464dae2f0ff | Python | 1,304 | 30 | import pandas as pd
import os
import sys
import pdb
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from app import create_app, db
from app.models import Image
from config.globals import ENVIRONMENT
... |
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