sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a1031581194e519218d1c2f1c0eb2ffc70856d1cf2b6f05bf05ee57ca1bebd71 | Python | 3,595 | 98 |
""" Create an organ mesh template from all segementation masks in the training
set. """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import os
import nibabel as nib
import numpy as np
import trimesh
from tqdm import tqdm
from scipy import ndimage
from skimage import measure
DATA_PATH = "/path/... |
ceeb8bc2447e8e76537f09312680e9c434af7f5b6ec046fbfa0a1688845834a2 | Python | 3,600 | 119 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
2d8846290dfff34c7bcf376b8c775f1ca957bff39479d78762e80925ee6ad64a | Python | 3,601 | 100 | from __future__ import annotations
import argparse
import json
from pathlib import Path
import numpy as np
import pandas as pd
def _weighted_mean(values: np.ndarray, weights: np.ndarray) -> float:
return float(np.average(values, weights=weights))
def _pv_brr_mean_and_standard_error(
plausible_values: np.n... |
b5dc38af7a7d748d77948a6d916944c7778fec072d5b21699a9404f85e45c999 | Python | 3,603 | 112 | import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
def plot_dsc(dend,name, corr=0):
d=dend
corrected=corr #use uncorrected to check against data
df=d['data']
peaks=d['peaks']
fig, ax1 = plt.subplots()
if corrected==1:
ax1.p... |
fe5b3534e0272c6cb3087e37083c75520e13bd6add2efd392a599b688094fa6b | Python | 3,603 | 74 | #!/usr/bin/env python
# Copyright 2017-2014 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
31cbc3445339a7a4e33c56d601f4c5f1e8774a37c1639f46bb4d23a2b07e4fe0 | Python | 3,609 | 133 |
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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-... |
d173c34795f0e492b3232f2f2c8ed7b0ab99c22411a3a5ae79389a680ba232ff | Python | 3,609 | 109 | # @File(label="Input directory", style="directory") src_dir
# @File(label="Output directory",style="directory") out_dir
# @String(label="Process filenames containing",description="Clear for no filtering",value=".tif") filenameFilter
"""
Process_Folder_PY.py
IJ BAR https://github.com/tferr/Scripts
This python sc... |
61cbb8074d5ecc2cb1d5bfe16b02451649d52bf2f4f1b70c39108a2837b76c31 | Python | 3,612 | 96 | #!/usr/bin/env python3
#
# Copyright (c) 2023 10X Genomics, Inc. All rights reserved.
#
"""Cell Typing utility functions."""
import json
import os
import pathlib
import cellranger.matrix as cr_matrix
from cellranger.rna.library import GENE_EXPRESSION_LIBRARY_TYPE
ALLOWED_GENOMES = ["GRCh38", "hg19", "mm10", "GRCm39"]... |
50c3ee11302eb8b16b93e86ce25332dc22d8eafbe86e3faeabde0476978ae576 | Python | 3,614 | 122 | """
Insect Brain DB
===============
<!-- difficulty: beginner -->
Fetch neurons and brain meshes from the Insect Brain Database.
The insect brain database (<https://insectbraindb.org>) is an online repository for neuron morphologies, brain regions and experimental
data across various insect species. At the time of wr... |
f9d02e72386a34901b5e8397fefc3387f132c68cadceaf439083f65fc8cccaa7 | Python | 3,623 | 93 | import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
import seaborn as sns
df = pd.read_csv('motion.csv')
MOTION_COLS = ['Trans_X', 'Trans_Y', 'Trans_Z', 'Rot_Pitch', 'Rot_Yaw', 'Rot_Roll']
def subtract_first_volume(group):
"""Subtract the first volume's parameters from all volumes in a bl... |
9eea44308a7871983bb0f5927ad72168be06d15294f5762cccc8127312b2076e | Python | 3,624 | 110 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
import json
import os
import os.path
import subprocess
import tempfile
import martian
import tenkit.log_subprocess as tk_subproc
__MRO__ = """
stage VLOUPE_PREPROCESS(
in string pipestance_type,
in string samp... |
a1746ba5abe4154bcae5b444acdec91222ac55bfff709a3bb2aa67c5a509f684 | Python | 3,624 | 111 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
The MCS class from Perses shamelessly wrapped and used here to match our API.
"""
from gufe.settings.typing import AngstromQuantity
from openff.units import Quantity, unit
from openff.... |
0cdf0cf34fed2dbbce15261074f07a9153231cb793e0afde379030760e833e24 | Python | 3,633 | 99 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its affiliates.
import argparse
import os
from itertools import chain
import cv2
import tqdm
from detectron2.config import get_cfg
from detectron2.data import DatasetCatalog, MetadataCatalog, build_detection_train_loader
from detectron2.data import detection_uti... |
e4927e85665fdc59d3e7c0d19f0112c37ef3f6225d23d3bf861617a02ad73038 | Python | 3,634 | 106 | """Tests for `navis.graph.graph_utils.propagate_labels`.
These pin down the *return type* of `propagate_labels`, which used to be inferred by
pandas/numpy and therefore varied with the installed pandas version: `Series.map()` on
string labels yields an `ArrowStringArray` under pandas >= 3 (where `future.infer_string`
... |
136e4d7d6b3678c735ef91e97faa65539641bfc11f11aa19eb8b624cc596c52c | Python | 3,638 | 112 | import numpy as np
def violin_prune_outliers(ax, data_list, positions=None, widths=0.7,
violin_kwargs=None,
whisker_kwargs=None,
outlier_kwargs=None,
median_kwargs=None,
... |
5dde301fa02e040e5b46c5f3c0ef9d98b0b3901ddf86055f0703b5e170f136f3 | Python | 3,638 | 111 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import numpy as np
import pytest
from openff.units import unit
from openfe.protocols.openmm_rfe import equil_rfe_settings
# afe settings currently have no FloatQuantity values
from openfe.... |
7083c9d2f18b669a00f598859af61cf705a80d0ec353d8214874ebb3cf948a6e | Python | 3,647 | 94 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
import unittest
import torch
from detectron2.modeling.box_regression import (
Box2BoxTransform,
Box2BoxTransformLinear,
Box2BoxTransformRotated,
)
from detectron2.utils.testing import random_boxes
logger = logging.getLogger(__name__)
clas... |
a3d5412d17c56f2047deffbc1bbc906fa73eea5511ec9e262a86c160fc8a2fe5 | Python | 3,649 | 104 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from gufe import SmallMoleculeComponent
from rdkit import Chem
from rdkit.Chem import AllChem
import openfe
from openfe.setup.atom_mapping import LomapAtomMapper
from .conftes... |
708bf9d9eb04bf88642bb2a31345cc6d1a6f438b2c1b3c0dd92835eee2beb2a5 | Python | 3,650 | 103 | #%%
from os import listdir
from os.path import join
import arviz as az
import pandas as pd
import mne
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from natsort import natsorted
import sys
sys.path.append('/mnt/obob/staff/fschmidt/cardiac_1_f')
from utils.plot_utils import plot_corr_topo
... |
824a58a11c37b34e578982e9358928be6da3635366a7d9f2f3384d91ecbd7b17 | Python | 3,651 | 105 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import json
import shutil
import h5py as h5
import martian
from six import ensure_binary
import cellranger.analysis.io as analysis_io
import cellranger.h5_constants as h5_constants
import cellra... |
1358845682558fff18c4a68cdfc3ebb13b5bdfe6cebd715dc39493d68f7f83e6 | Python | 3,654 | 134 | """ Test datasest """
import pytest
import numpy as np
from brainspace.datasets import *
from brainspace.vtk_interface.wrappers import BSPolyData
parametrize = pytest.mark.parametrize
testdata_surface = [
({}),
({'as_sphere': True}),
({'as_sphere': False, 'with_normals': False}),
({'as_sphere': ... |
d5e99d09cbbe80f1a8219b37eee1ed3a6541500186ca42259af1edbee82bf8c1 | Python | 3,657 | 101 | from __future__ import annotations
import io
from collections import OrderedDict
from io import StringIO
from pathlib import Path
from typing import Any
import pytest
from hypothesis import given
from hypothesis import strategies as st
from pyfakefs.fake_filesystem import FakeFilesystem
from pytest_mock import Mocker... |
aa00c2b197d8db32487a2529b457fff31366ed6c1991667a1676f25f7117d978 | Python | 3,661 | 74 | import os
import pandas as pd
import collections
import pyranges as pr
# Load the TSV file into a DataFrame
file_path = "/home/nomura/Proj/mmvelo/experiments/SHARE-seq_hf/2023-08-03T13:31:54_nb_k50_for_analysis/downstream_analysis/result/GRN_inference_sep/network_filtered_fdr_1e-4_bh.tsv"
data = pd.read_csv(file_path... |
5a6f810fdadae199205a82a3153cc1d078db46e7b3f2b24b9725ab5e98300691 | Python | 3,664 | 129 | from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
results_dir = Path("ana/results_20260331")
file_paths = sorted(results_dir.glob("s*/summary_thresholds.csv"))
# ターゲット条件
target_layer = "conv1"
target_ecc = "ecc12"
max_r = 150
# CSVの component 列と direction 列に対応する表示順
con... |
47012faae9240228240500ecffe46de9d0b8b0d6f3d384591664bf968e3ff8a1 | Python | 3,677 | 73 | import torch
from torch._dynamo import OptimizedModule
from torch.nn.parallel import DistributedDataParallel as DDP
import torch.distributed as dist
from nnunetv2.utilities.ddp import get_ddp_topology
def load_pretrained_weights(network, fname, verbose=False):
"""
Transfers all weights between matching keys ... |
4d242736cb60666d9daece0124982c36db62666b85707f2019ad26051aa41d8f | Python | 3,681 | 131 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Custom OpenMM Forces
TODO
----
* Add relevant duecredit entries.
"""
import numpy as np
import openmm
def get_boresch_energy_function(
control_parameter: str,
) -> str:
"""
... |
f15fa739d33033f27cd730372a083d66c120572140ec7e201d5019f3f72420cc | Python | 3,690 | 110 | """Tests for membership storage."""
from mesa import Agent, Model
from mesa.meta_agents import MetaAgents
from mesa.meta_agents.backend import MembershipBackend
def test_add_and_query():
"""Add edges and verify basic query behavior."""
backend = MembershipBackend()
backend.add_membership("a1", "g1", "mem... |
3a11fb3dd3e23ee716c8146f9c22d3c32fe5ad3b596c4beddc2ecc09a54bd229 | Python | 3,694 | 73 | #!/usr/bin/env python
# Copyright 2017-2018 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
56a8f26f7aaa48009fe84c43ddfb57c957aac6a2d3919ea4144fa5129ad142d0 | Python | 3,694 | 84 | #wget "https://rest.uniprot.org/uniprotkb/stream?download=true&format=fasta&includeIsoform=true&query=%28%28proteome%3AUP000005640%29%29"
#python sequenceVenn_fasta.py CCDS_nucleotide.20221027.fna.CCDS.20221027.txt.aa.fasta uniprotkb_proteome_UP000005640_2026_05_17.fasta --write-fasta
import argparse
from pathlib impor... |
ed4da0472422d12c8ae2aa318cf63d52fcd548b5d5c2cb5ae8f097ab44fd4bc2 | Python | 3,694 | 104 | #python mqrunDash_verify_peptides.py
from pathlib import Path
import re
import mqrunDash as mq
import argparse
parser = argparse.ArgumentParser(description="Verify mqrunDash peptide label claims against a FASTA and DuckDB file.")
parser.add_argument('--db', default=r'Z:\Download\mqrun.duckdb', help='Path to the Duck... |
a664f2c124e8c2e7504a03d64a8d4519577a1e0ed1ce2eabd1eedb75fa0e53ff | Python | 3,697 | 114 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Barcode detection classes for single-cell and spatial tr... |
67e53a95314c4fd8d96e350d5e46d89f6b8bb782b1f1b5e76192d9baecf3e0df | Python | 3,700 | 116 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import MDAnalysis as mda
import numpy as np
import pytest
from openff.units import unit
from openfe.protocols.restraint_utils.geometry.boresch.guest import (
_bonded_angles_from_pool,
... |
ff28960d96c1835cbc107e12494f5c2c4a3b6ccdcea3d61401853323e724440c | Python | 3,702 | 99 | #
# Copyright (c) 2025 10X Genomics, Inc. All rights reserved.
#
"""Multiplexing cell typing methods."""
import martian
import cellranger.cr_io as cr_io
from cellranger.cell_typing.common_cell_typing import CellTypeResults
__MRO__ = """
stage CELL_TYPING_MULTIPLEXER(
in bool disable_cloud_cell_types... |
0bad28c8830db1857b1783fdde6adddb027be2159bdfa525df7943565e6810a9 | Python | 3,708 | 96 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import torch
from torch import nn
from detectron2.config import CfgNode
from detectron2.layers import ConvTranspose2d, interpolate
from ...structures import DensePoseChartPredictorOutput
from ..utils import initialize_module_params
from .registry impo... |
1ede0b3861d063dff284a91d3af790d31f3610dbf6e76ccaf4bf5eb3dc74620b | Python | 3,709 | 118 | from __future__ import annotations
import argparse
import sys
from collections.abc import Callable, Iterable
from typing import (
TYPE_CHECKING,
Any,
Generic,
TypeAlias,
TypedDict,
TypeVar,
overload,
)
from typing_extensions import Required, Unpack
if TYPE_CHECKING:
from argparse impo... |
b8512a9c4862c291fc855609d9fcccd8f71e17c62ac08062fa15df80ea20db84 | Python | 3,711 | 91 | import pydoc
import warnings
from typing import Union
from nnunetv2.utilities.find_class_by_name import recursive_find_python_class
from batchgenerators.utilities.file_and_folder_operations import join
def get_network_from_plans(arch_class_name, arch_kwargs, arch_kwargs_req_import, input_channels, output_channels,
... |
0b5ecfc6841c91253d5791a98907f201c127c7b5408faae5b3060551cff584d8 | Python | 3,715 | 105 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from support.config import ALGORITHMS, ALGORITHM_LABELS, COLORS, METRICS
from support.plot_helpers import tables, xerr
def prepare_data(results_or_tables) -> pd.DataFrame:
candidates = tables(results_or_tables)["candidate_model_selection"].co... |
40c7084010e81b05bb9ea96be9bfcb2fb9fe27f761e8cb0cddef182fdf5847e0 | Python | 3,724 | 100 | import os
import sys
import glob
import numpy as np
import nibabel as nib
def hide_files(directory_use, dwifile, dwibasename, suffix):
hidden_dir = os.path.join(directory_use, suffix)
if not os.path.exists(hidden_dir):
os.makedirs(hidden_dir)
os.rename(dwifile, os.path.join(hidden_dir, dwifile))
... |
23775c63ba6eb7cbb140e763d5ff9c92eb730a542109974e77f795316b19a3cb | Python | 3,725 | 98 | #!/usr/bin/python3
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "So... |
a483a49110b2428c6bc82e2de55f4313499073a31a7856568dcd01c3b45b9614 | Python | 3,733 | 111 | import ldscore.ldscore as ld
import unittest
import bitarray as ba
import numpy as np
import nose
import ldscore.parse as ps
def test_getBlockLefts():
l = [
(np.arange(1, 6), 5, np.zeros(5)),
(np.arange(1, 6), 0, np.arange(0, 5)),
((1, 4, 6, 7, 7, 8), 2, (0, 1, 1, 2, 2, 2))
]
for c... |
ca708de7e48ad7eb83090419bc1cd8cf0265abef412edb1ef312542a1d9af339 | Python | 3,739 | 84 | import os
import sys
import glob
import pandas as pd
import math
import matplotlib.pyplot as plt
import scvelo as scv
import anndata as ad
import numpy as np
import scanpy as sc
import scipy
import time
from .TSvelo_pp_utils import get_TFs, select_gene, geneid_symbol
def read_data(args):
if args.dataset_name == '... |
18b0e6d5dc74aeeabca0960f089f2e6e8308d0eea3403d44378054102df23d44 | Python | 3,740 | 68 | from batchgenerators.utilities.file_and_folder_operations import *
import shutil
from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
from nnunetv2.paths import nnUNet_raw
def convert_amos_task1(amos_base_dir: str, nnunet_dataset_id: int = 218):
"""
AMOS doesn't say anything abo... |
580355dd358b41224aa6ba473cb66234905a9e69c1842b125f9a4d53c2f74fba | Python | 3,742 | 126 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import matplotlib.pyplot as plt
import os, sys
import numpy as np
import scipy.io as sio
np.seterr(divide='ignore', invalid='ignore')
import seaborn as sns
def intersect_mtlb... |
c0c74df39d5a216ad8d5a06132b84e7575966b64426450815f45ca7ceab20309 | Python | 3,742 | 81 | '''
Created on Sep 18, 2025
@author: voodoocode
'''
import numpy as np
import nibabel
import scipy.ndimage
import scipy.io
import scipy.interpolate
TRANS_PATH = "/home/voodoocode/Downloads/sub-Ba01slicer/normalization/transformations/sub-Ba01slicer_from-MNI152NLin2009bAsym_to-anchorNative_desc-ants.nii.gz"
#TRANS_... |
56dd4465c797e71040dc35bcb8c3cf8fe1782a7e7a879f20384f2dc3b47cc502 | Python | 3,750 | 100 | import glob
import os
import json
import pandas as pd
from pathlib import Path
from ..utils import load_checkpoint
import numpy as np
# Import the metric calculation logic
from ..utils.evaluation_metrics import compute_macro_f1_and_ci
PKG_ROOT = Path(__file__).resolve().parents[1]
MODELS_DIR = PKG_ROOT / "semantic_mod... |
e1a4357fd1af8476ebbe8ff7a10157e8a50fa1527c8ead6e027e2526891a9e3b | Python | 3,750 | 58 | import os
import nibabel as nib
import numpy as np
from nilearn import image, plotting
from nilearn.maskers import NiftiMasker
from nilearn.signal import clean
from tristan_pipeline.io.params import *
from tristan_pipeline.utils.loading_utils import *
from tristan_pipeline.utils.preproc_utils import *
from tristan_pipe... |
6091bc094ddd23eee8afc0103ea4e6034dc795e1dd5c90919e95cb8786ec050f | Python | 3,752 | 90 | import os, argparse, sys, datetime
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
#Prevent JAX from using all of the threads available
os.environ["OMP_NUM_THREADS"] = "1" # export OMP_NUM_THREADS=4
os.environ["OPENBLAS_NUM_THREADS"] = "1" # export OPENBLAS_NUM_THREADS=4
os.environ["MKL_NUM_THREADS"] = "1" # export MKL_NUM_... |
c8bb9c9f8795dfb3f2969d7da8ce2130db2059155559508fb7fffd5a830f3efc | Python | 3,754 | 74 | from matplotlib import pyplot as plt
import numpy as np
import os
import pickle
from rCPGswCPG.plotting_figures.plotting_utils import run_sim, resample, plot_recordings
from rCPGswCPG.utils.gen_utils import get_project_root
if __name__ == '__main__':
rerun = True
modes = ['eupneic', 'apneustic']
# settle t... |
30678478d62ff004cbea54da957a5ce189db394b7b957bd2b283a7f01d896484 | Python | 3,756 | 112 | #!/usr/bin/env python
#
# Copyright (c) 2024 10X Genomics, Inc. All rights reserved.
#
"""Postprocess the cell type diff expression generated.
Rewrite the header of the cell types diff expression csv to have the celltypes
and generate the figure for websummary.
"""
import json
import os
from dataclasses import asdic... |
bc12323b73d386c8e503da3a2585fe3a79bdfd4267791dcba21e0de0a4af55a9 | Python | 3,759 | 97 | from typing import Callable
class ValueFormatter:
@staticmethod
def _formatted_value(value) -> str:
if isinstance(value, dict):
return ValueFormatter.dict_method()(value)
elif isinstance(value, list):
return ValueFormatter.list_method()(value)
elif isinstance(va... |
d906e79d340ce99e2a8943c558871c92ab2892822889f482351a5ac885d48149 | Python | 3,759 | 117 | """ Created on Tue Aug 27 15:18:40 2024
@author: dcupolillo """
import sys
from PyQt5 import QtWidgets
from PyQt5.QtWidgets import QMainWindow, QGridLayout, QWidget, QMessageBox
from ROIpy.GUIv2.load_frame import LoadFiles
from ROIpy.GUIv2.plot_structures_controller import StructureFrame
from ROIpy.GUIv2.scan_para... |
dded73e11078187b57e03764e853a2a51673ccd291b4be3f03486bfd0dd7c278 | Python | 3,759 | 119 | import pandas as pd
data = pd.read_csv('F:/OneDrive - NTNU/UTR/data2.csv')
data.head()
data.describe()
import numpy as np
data['RFPlog']=np.log2(data['Fluorescence'])
data['RFPlog'].hist()
data['ReadsLog']=np.log2(data['#Reads Col'])
data['ReadsLog'].hist()
import matplotlib.pyplot as plt
plt.scatter(data['RFPlog'],d... |
07b105b7246f8ec955134e551effb64d2facc3cf2127356db93ecd01ee9e7d23 | Python | 3,764 | 105 | #!/usr/bin/env python
#
# Copyright (c) 2018 10X Genomics, Inc. All rights reserved
#
from __future__ import annotations
import os
from typing import TYPE_CHECKING
import martian
import cellranger.cr_io as cr_io
import cellranger.feature.crispr.protospacer_calling as protospacer_calling
if TYPE_CHECKING:
impor... |
407367b50fe947e0c5ac9a559fe43470b2113e371fc8bf6b0adbf43e1fd9d512 | Python | 3,764 | 94 |
# %% Imports
# Imports from the library
from micorr.simulation import simulations, testing, plotting, transformations
from micorr.estimators import mi_estimators
# More general imports
import numpy as np
import matplotlib.pyplot as plt
# %% Initial parameters
# Simulating the base evoked response
sim_params = {'st... |
6abb37002bb21653d24a9edcc532cc30c1eb307249acb49ea2089c0f05dcfe0b | Python | 3,764 | 109 | """"
Created on 06.04.2019
@authors: Niklas Pallast
"""
import os
import sys
import argparse
import numpy as np
import nibabel as nii
def getOutfile(roi_file,img_file):
imgName = os.path.basename(img_file)
baseName = str.split(os.path.basename(roi_file),'.')[0]
dtiParam = str.split(imgName,'.')[-3]
... |
bfd2e71f3854750dbb59597dd4dbf4b7e49d82ddc82fdba6dda512ed8f36fc68 | Python | 3,764 | 102 | #!/usr/bin/env python3
#
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
# Inject barcode (CB) and UMI (UB) ... |
ec2c8dd6471de5184a07b56e1eff98332c3f9c7553a490f6524ac0e5ff47c613 | Python | 3,770 | 81 | from typing import Dict
import pytest
import numpy as np
from brian2 import Network, seed
from brian2.units import msecond, mvolt, nsiemens, hertz
from hsnn.core import NeuronClass, SynapseClass, Projection
from hsnn.core.config import ModelParams
from hsnn.core._brian2.groups import COBAFactory
@pytest.fixture(aut... |
ce8ad6bc99fbc0ef52a56e022ed0a167cf207a5cf0925875092ad705e9aad41d | Python | 3,771 | 106 | from __future__ import annotations
import argparse
import json
from pathlib import Path
import pandas as pd
REPLICATE_WEIGHT_COUNT = 80
def _read_student_file(path: Path) -> pd.DataFrame:
suffix = path.suffix.lower()
if suffix == ".csv":
return pd.read_csv(path, low_memory=False)
if suffix == ... |
f2ad2b44410f706e3ba8ebbcfcdf1ced795ddc1a9d2e9d6e71edca6aa7f6b561 | Python | 3,771 | 112 | """Optional tautomer step tests."""
from __future__ import annotations
import sys
import pytest
from rdkit import Chem
from src.tautomer.base import TautomerError
from src.tautomer.factory import build_tautomerizer
from src.tautomer.rdkit_adapter import RDKitTautomerizer, enumerate_tautomers
def _canon(smiles: st... |
a6e7f500556afa4710d0b5c050be8a84e20f78bd813a2c25aab72378e3b665c2 | Python | 3,773 | 99 | """
Brain Image Library
===================
<!-- difficulty: beginner -->
Fetch neurons from the Brain Image Library (BIL).
The Brain Image Library (<https://www.brainimagelibrary.org>, BIL) is a public repository hosted at the Pittsburgh
Supercomputing Center. It is primarily known for its (very large) microscopy da... |
41c04bacefa66cfea7c878630c72c2785bb1323c7366cd5eea67ca04c9e1d6c5 | Python | 3,780 | 118 | #!/usr/bin/env python3
"""
Fast duplicate file finder.
Scans a start directory (default $HOME), groups files by size, hashes files with same size
using xxhash if available (falls back to sha1), and writes a CSV of duplicate files
(sorted by size descending).
Output CSV columns: group_id,hash,size,duplicate_count,path
... |
7e7ed839a33df335a477a97fcc8aba9c3046175d512455a58727067d24adbcdc | Python | 3,781 | 109 | import subprocess
import numpy as np
import itertools
import argparse
import logging
import re
def get_current_gpu_utilization():
"""
From: https://discuss.pytorch.org/t/access-gpu-memory-usage-in-pytorch/3192/3
Get the current gpu usage.
Returns
-------
usage: dict
Keys are device ids... |
32195ec889591109600a7367510f98340b7fa04af08cb4842f558f7fccf8f46e | Python | 3,783 | 113 | import gzip
import pickle
from pathlib import Path
from typing import Any, Mapping, Optional, Tuple
import pandas as pd
from omegaconf import DictConfig, OmegaConf
from .data import ImageSet
from ..transforms import transform_registry, Compose
BASE_DIR = (Path(__file__).parents[3]).resolve()
DATA_DIR = BASE_DIR / 'd... |
e670334d75751cd6ae5dd6834153fe71f32dd90d87bacab3c6f329b6907ba247 | Python | 3,786 | 129 | #!/usr/bin/env python
#
# Copyright (c) 2017 10x Genomics, Inc. All rights reserved.
#
import csv
import os
import shutil
import martian
__MRO__ = """
stage PARSE_PARAM_CSV(
in csv params_csv,
out csv params_csv,
out int num_analysis_bcs,
out int random_seed,
out int num_pca_bcs,
... |
31f5b4d63639fe3765a8091fb160df2bc1d72556e9204ae31fe65e2d6ba6f9c5 | Python | 3,791 | 100 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from dataclasses import make_dataclass
from functools import lru_cache
from typing import Any, Optional
import torch
@lru_cache(maxsize=None)
def decorate_predictor_output_class_with_confidences(BasePredictorOutput: type) -> type:
"""
Create a... |
72d8cbd5f805358d9275e04f4d0d7535a3495f631abbfe740b017a547ab8ccd8 | Python | 3,801 | 109 | import logging
from typing import Iterable
import torch
from torch import Tensor
from chemprop.data import BatchMolGraph, MulticomponentTrainingBatch
from chemprop.models.model import MPNN
from chemprop.nn import Aggregation, MulticomponentMessagePassing, Predictor
from chemprop.nn.metrics import ChempropMetric
from ... |
944cedccc7c471bced0aadcd861fab7bc84e9c08c571ab3e0da9947f204e4be3 | Python | 3,802 | 81 | # Copyright 2021 HIP Applied Computer Vision Lab, 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... |
b735f15a49d98304d485c627ba7da2325b230a9e83b555931cbefd6ae9bdc73a | Python | 3,802 | 100 | from pathlib import Path
from typing import List, Dict
from dataclasses import dataclass
import numpy as np
import torch
import torchvision.transforms as transforms
import matplotlib.pyplot as plt
from abx_app.AttackCNN.attack_examples import run_attack
from . import config
from .utils.activation_manager import Acti... |
4a0d47682f2c0439eaeda66dbe8f8645550e0435437114b285882111eb6787d9 | Python | 3,805 | 93 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import numpy as np
from typing import List, Optional, Tuple
import torch
from detectron2.data.detection_utils import read_image
from ..structures import DensePoseChartResult
from .base import Boxes, Image
from .densepose_results import DensePoseResults... |
270310f73c8b80187b1e48eb4164f0aa5df9a9e4cc3d1e92b7a4c472f5124ac4 | Python | 3,806 | 91 | import numpy as np
def merge(dict1, dict2):
keys = np.unique(list(dict1.keys()) + list(dict2.keys()))
keys = np.unique(keys)
res = {}
for k in keys:
all_configs = []
if dict1.get(k) is not None:
all_configs += list(dict1[k])
if dict2.get(k) is not None:
... |
57905b094e79deb169cfdb298ada250b8afd112a6c33ca65a454e5dab2c64b3c | Python | 3,807 | 109 | # Copyright (c) Facebook, Inc. and its affiliates.
import os
import tempfile
import unittest
import yaml
from omegaconf import OmegaConf
from omegaconf import __version__ as oc_version
from dataclasses import dataclass
from detectron2.config import LazyConfig, instantiate, LazyCall as L
from detectron2.layers import ... |
764ca715f90574f32909f71f379906a5f4673e88fde30413f78f4e7dff7babfb | Python | 3,807 | 92 | # python ionSearch.py
import pandas as pd
import xml.etree.ElementTree as ET
import numpy as np
import os
#Load and filter data
chargeThreshold = 1000
intensityThreshold = 1
dirPath="L:/promec/HF/Lars/2025/251204_Maren_Gemma/combined/txt/"
mzData = pd.read_csv(dirPath+"matchedFeatures.txt", sep='\t')
ionSelect = pd.rea... |
025136feead71ea7b185761121e3022d6ca2554da9df186501e70f3f01e8ea6d | Python | 3,810 | 104 | """Process-level cache for loaded model weights.
Batch workflows construct a ``Predict`` object per file, and each construction
otherwise repeats ``torch.load`` + ``load_state_dict`` + a host-to-device copy of
the same checkpoint. Caching the built model keeps repeated predictions on one
checkpoint from paying that co... |
47ac4be2820df2a6405dc822ae7ec34d02129af066d0a4dc1ea9fae467bcb495 | Python | 3,827 | 99 | """Global configuration for figure generation scripts.
All paths are relative to the repository root. No hardcoded absolute paths.
"""
from pathlib import Path
# Repository root: two levels up from python/utils/
REPO_ROOT = Path(__file__).resolve().parents[2]
DATA_DIR = REPO_ROOT / 'data'
OUTPUT_DIR = REPO_ROOT / 'ou... |
82cd9b9494db7773d244799fc3fb16b1e3160f10068057c8702b4fc5c951e278 | Python | 3,828 | 95 | ## Setup GENTRL Deep learning enables rapid identification of potent DDR1 kinase inhibitors https://www.nature.com/articles/s41587-019-0224-x
#https://docs.anaconda.com/anaconda/install/linux/
#! sudo apt-get install python3 libxrender1 libxext6 libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 lib... |
aada734f8530caddf337d3624c279a007d26eb28e3160d1d1bb223816659fc51 | Python | 3,830 | 143 | """Utilities for the aperiodic-clinical project."""
from collections import Counter
import numpy as np
import pandas as pd
from specparam.utils import trim_spectrum
####################################################################################################
##################################################... |
ae67ed5aecd87b607cbf58ec4074ceb39badfdc44a71176db0367eaada839c9d | Python | 3,839 | 141 | """NOTE: these tests make a lot of assumptions about the internal mechanics of the AtomFeaturizer,
so they'll need to be reworked if something ever changes about that."""
import numpy as np
import pytest
from rdkit import Chem
from rdkit.Chem.rdchem import HybridizationType
from chemprop.featurizers import MultiHotAt... |
6c80e2e939cd5b3625f56b0b76b267ef236585d84892661bbdf79f5e7ab6807e | Python | 3,842 | 108 | import statsmodels.api as sm
import pandas as pd
import numpy as np
import pymc as pm
import aesara.tensor as at
def aggregate_sign_feature(df_in, feature_key, pos_mask):
'''
Aggregate data across channels per subject for each feature of interest.
'''
feature_by_age = []
for subject in df_... |
db0b0801cde13049d3053b0d347295104da2d56891956899300c86cdf168e4ed | Python | 3,843 | 103 | # Copyright (c) Facebook, Inc. and its affiliates.
import torch
from torch import nn
from torch.autograd import Function
from torch.autograd.function import once_differentiable
from torch.nn.modules.utils import _pair
from detectron2.layers.wrappers import disable_torch_compiler
class _ROIAlignRotated(Function):
... |
d569628ad1c05be56b1d66cf702db1e145ba2d3a5e4fae02dea513019750e433 | Python | 3,845 | 108 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import numpy as np
from typing import Iterable, Optional, Tuple
import cv2
from densepose.structures import DensePoseDataRelative
from .base import Boxes, Image, MatrixVisualizer, PointsVisualizer
class DensePoseDataCoarseSegmentationVisualizer:
... |
ef47a1899b47f8e44b7d135c6aae9f15ce674b767417726e20599b245a5380ff | Python | 3,848 | 72 | ############################################################
# ---------- NBS Consensus Clustering Functions ---------- #
############################################################
import os
import pandas as pd
import numpy as np
import scipy.spatial.distance as dist
import scipy.cluster.hierarchy as hclust
# Takes... |
f85e7cdadb3b14e90a8a687fb2549847fc521c0d45187d06c7152f79443a5242 | Python | 3,849 | 142 | from navis import Dotprops
import pytest
import numpy as np
from navis.nbl.smat import (
Digitizer, LookupNd, Lookup2d, LookupDistDotBuilder
)
SMALLEST_DIM_SIZE = 3
SEED = 1991
def lookup_args(ndim):
f"""
Create arguments for an ND lookup table.
The first dimension is of size {SMALLEST_DIM_SIZE},
... |
2265813639c01bfede73c6754ef322ff3c17ad6e2e331b9b6a169297f397fd5c | Python | 3,851 | 77 | import os
import glob
import numpy as np
import pandas as pd
import anndata as ad
import numpy as np
import scanpy as sc
import time
import matplotlib.pyplot as plt
from TSvelo.TSvelo_utils import run_paga, run_palantir, get_colors, show_imgs, sigmoid, relu, scv_analysis
from TSvelo.TSvelo_pp import preprocess
from TSv... |
65c00e4bcd90d7f64c09026ec6445f2c706ec0cec3697e2d54bbccb04cb871ee | Python | 3,851 | 122 | from __future__ import annotations
import argparse
import logging
from pathlib import Path
from typing import Any
import attrs
from snakebids import bidsapp
from snakebids.bidsapp.args import ArgumentGroups
from snakebids.plugins.base import PluginBase
from snakebids.utils.utils import DEPRECATION_FLAG
logger = log... |
02ae4f425b11294df6a8cdf4e9320a325a0a015e3e3dbb57bd77fd52fee3c8ee | Python | 3,853 | 164 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
"""Constants used by the VDJ pipeline."""
######################################################
# DO NOT add new items to this file.
#
# - If a constant is only used from a single module, put it in that module.
# - If a constant is... |
fadc2f8faf44aef926d64941b9ba020cf748503ca4b600dc86c17e8a4ab0ac78 | Python | 3,853 | 101 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 9 12:13:33 2022
@author: evanqu
"""
import numpy as np
import gzip
import pickle
import logging
import argparse
from accusnv import log as accusnv_log
from accusnv.preprocessing import utils as ghf
log = logging.getLogger('accusnv')
def vcf_to_qu... |
0e996b8a9945ed98fec4281ed13ce37a1b584331261ae98ab6e75b8c402c19f6 | Python | 3,862 | 106 | # ------------------------------------------------------------------------------
# Title: Gene Regulatory Network Inference (GRNBoost - P0)
# Author: Yiran Song
# Date: March 18, 2025
# Description:
# This script runs GRNBoost2 to infer gene regulatory networks from Commot spatial communication data.
#
# Key Functions:... |
313038101d737d87997c66b25872cd0d2787bc3aac9650fc4fd19e5554f1f589 | Python | 3,868 | 107 | # Copyright (c) Facebook, Inc. and its affiliates.
import torch
from torch import nn
from torch.nn import functional as F
from torch.nn.modules.utils import _pair
from detectron2.layers.wrappers import _NewEmptyTensorOp
class TridentConv(nn.Module):
def __init__(
self,
in_channels,
out_ch... |
889bdc1a66289683890d79e774ecc5193a0587e69a2604bd0339a42dd1b18b2d | Python | 3,868 | 100 | # ## Manually export images using the picasso functions to render oversampled images with optional precision based blur.
from configparser import Interpolation
import os
import numpy as np
import pandas as pd
from picasso import render, io
import matplotlib.pyplot as plt
from skimage.io import imread
import matplotlib.... |
ec11b50c65a571973ed548f5d46572edffc4c7a6f2f2d26129260b1596c81909 | Python | 3,868 | 99 | from __future__ import annotations
from dataclasses import dataclass
from datetime import datetime, timezone
from math import ceil
from pathlib import Path
from textwrap import fill
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from rdki... |
4db2f06a954efeb51e4364e70096224a661234a456c75b60d6ad4405b8863735 | Python | 3,879 | 74 | #coding https://mattmazur.com/2015/03/17/a-step-by-step-backpropagation-example/ with tensorflow/keras, checking with iterative version at https://github.com/animesh/ann/blob/master/ann/Program.cs with following output
#Iteration = 1 Error = 0.298371108760003 Outputs = 0.751365069552316 0.772928465321463
#... |
6af592fcfcf975dde43bea71c8f0fc58b9949f5a9a381d6a819b21eee82104f6 | Python | 3,882 | 98 | import numpy as np
class LambdaWarmUpCosineScheduler:
"""
note: use with a base_lr of 1.0
"""
def __init__(self, warm_up_steps, lr_min, lr_max, lr_start, max_decay_steps, verbosity_interval=0):
self.lr_warm_up_steps = warm_up_steps
self.lr_start = lr_start
self.lr_min = lr_min
... |
a607277dc423cd9997c01a6583d1e50f73c3cfdbd24c897e68909bc2f8bd9bb7 | Python | 3,882 | 122 |
#%% Imports
# Imports from the library
from micorr.simulation import simulations, testing, plotting, transformations
from micorr.estimators import mi_estimators, corr_est
# More general imports
import numpy as np
from functools import partial
#%% Initial parameters
# Dictionary with the estimators to be tested
est... |
850f563f3bd5d9a3be8ef19d05cb265dc0fe19c1fb0ca77bb7a84dcc862284f4 | Python | 3,883 | 101 | import torch
import torch.nn as nn
class UNet3D(nn.Module):
def __init__(self, n_in, n_out):
super(UNet3D, self).__init__()
# Encoder
self.ec0 = self.encoder_block( n_in, 32, kernel_size=3, stride=1, padding=1)
self.ec1 = self.encoder_block( 32, 64, kernel_size=3,... |
2d23e747c24e2a3dabc1c65ef8c288f4650141bd2283ffa0e7b79328b73a6f74 | Python | 3,891 | 115 | import logging
import os
import numpy as np
__all__ = ['check_can_write_file', 'normalize_3d_volume', 'volume4d_to_matrix']
def check_can_write_file(fpath: str, force: bool = False):
"""
Check if a file can be written.
The function checks if the file already exists, the user has the permission
to w... |
d14620a956d3e741fa094262fae5961d9993afd6454e6a4db3a0c8cbfba1d35f | Python | 3,899 | 111 | """Shared helpers for locating a reference genome and reading its stats.
Sample sheets and FASTQ paths are not handled here: the CLI resolves every read and reference
path up front and writes them into samples.csv, which the workflow reads directly."""
import os
import glob
import gzip
import numpy as np
from Bio imp... |
ffc6270eb285ff89496eb204d32f1635be05df678ed4d1e02e28dc1d0406ef86 | Python | 3,899 | 132 | """ Created on Tue Aug 27 15:22:29 2024
@author: dcupolillo """
from pathlib import Path
from PyQt5.QtWidgets import (
QMainWindow, QFrame, QLabel, QGridLayout,
QPushButton, QFileDialog, QMessageBox)
from PyQt5.QtCore import Qt, pyqtSignal
from ROIpy.core.structures import Stack, Morphology, Scanfields
c... |
aae50591e8ca91fff0358a5937943a7577e310c192951276bc1966df1428c1d1 | Python | 3,903 | 98 | # Copyright (c) Facebook, Inc. and its affiliates.
import contextlib
import os
import random
import tempfile
import unittest
import torch
import torchvision.io as io
from densepose.data.transform import ImageResizeTransform
from densepose.data.video import RandomKFramesSelector, VideoKeyframeDataset
try:
import ... |
039428d5edd73e261152b844725efdd5731b5abfba3fce420df6264395b62c7c | Python | 3,904 | 110 | from copy import deepcopy
from pathlib import Path
from typing import Any, Dict, Iterable, MutableMapping, Mapping, Optional, Sequence
import numpy as np
from omegaconf import OmegaConf
from ray import tune
from hsnn.utils import io
from hsnn.simulation import Simulator
__all__ = ["traverse_dict", "override_config",... |
16f213864381c3615c92f0b104f9295ab2133cdaa1941a83e0e117051db0623c | Python | 3,907 | 111 | # Copyright (c) Facebook, Inc. and its affiliates.
import itertools
import math
import operator
import unittest
import torch
from torch.utils import data
from torch.utils.data.sampler import SequentialSampler
from detectron2.data.build import worker_init_reset_seed
from detectron2.data.common import DatasetFromList, T... |
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