sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ef8c79a203b2a0adcdfac7068b12e0f780f6113d65800208fd15d2079c8a3c71 | Python | 982 | 24 | #python plotVenn.py comb-mntzDownloadMQ-mntzDownloadtesorAI-ProteinIDs-proteingroupid-iBAQ-intensityIBAQ.csv
#python plotVenn.py comb-mntzDownloadMQ-mntzDownloadtesorAI-ProteinIDs-proteingroupid-Top3-intensitytop3.csv
import sys
import pandas as pd
import numpy as np
from supervenn import supervenn
from matplotlib impo... |
66a9859873ed3b37ff2c668c379d595b3c20e3ba635db5b8ef87b2eecd4264b7 | Python | 987 | 31 | from fvcore.common.param_scheduler import MultiStepParamScheduler
from detectron2.config import LazyCall as L
from detectron2.solver import WarmupParamScheduler
from .cascade_mask_rcnn_mvitv2_b_3x import model, optimizer, train
from .common.coco_loader_lsj import dataloader
model.backbone.bottom_up.embed_dim = 144
... |
55afe294be8b1d8774c0a3f22f3bc893ea9d16302520939205ba588a07af24ca | Python | 988 | 28 | """Plugins for the ``fetch`` command"""
from openfecli.fetching import PkgResourceFetcher, URLFetcher
_EXAMPLE_NB_BASE = "https://raw.githubusercontent.com/OpenFreeEnergy/ExampleNotebooks/main/"
RBFE_TUTORIAL = URLFetcher(
resources=[
(_EXAMPLE_NB_BASE + "rbfe_tutorial/", "tyk2_ligands.sdf"),
(_E... |
69c305171ae2fce514966f075959c8f77fce891e6a8b2603638789bbdea22b58 | Python | 988 | 26 | from __future__ import annotations
from rdkit import Chem
from src.protonation.openbabel_adapter import OpenBabelProtonator
def _formal_charge(smiles: str) -> int:
molecule = Chem.MolFromSmiles(smiles)
assert molecule is not None
return sum(atom.GetFormalCharge() for atom in molecule.GetAtoms())
def t... |
0d4d7ef7a717342b48c1730c95dde7c428bf1bd66303f351e8581e6a1b6db348 | Python | 990 | 25 | # Copyright 2011-2014 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 obtain a copy of the Licen... |
a551863b9aeb475a4588d38d6f6687ffaa4f889af7b1409e88b12f17437ef6b2 | Python | 991 | 25 | from typing import Optional
import numpy.typing as npt
import numpy as np
from scipy import stats
def uniform(points: npt.NDArray[np.float_], p_conn: float = 1,
num_conn: Optional[int] = None) -> npt.NDArray[np.int_]:
if num_conn is None:
return np.flatnonzero(np.random.rand(len(points)) < p_... |
aff3bbec36d5f7b0ccac097b27dcd0709befe2fc0e1a2aa260a911054b8c2098 | Python | 991 | 31 | import sys
from pathlib import Path
import numpy as np
SCRIPTS = Path(__file__).resolve().parents[1] / "scripts"
sys.path.insert(0, str(SCRIPTS))
from run_xgboost_shap import summarize_outer_test_tree_shap
class FakeExplainer:
def shap_values(self, features):
return np.asarray([[1.0, -2.0], [3.0, -4.0... |
467fdec5ac948edf1cac979b4681f45c92a164c88b1c47e52e56e9b81224bd4f | Python | 992 | 39 | from fvcore.common.param_scheduler import MultiStepParamScheduler
from detectron2.config import LazyCall as L
from detectron2.solver import WarmupParamScheduler
from .cascade_mask_rcnn_mvitv2_b_in21k_100ep import (
dataloader,
lr_multiplier,
model,
train,
optimizer,
)
model.backbone.bottom_up.emb... |
b5b3e4bf165f77d61497f7af01b0c76607f0a2a7adcb11f98cc66374cdb7549d | Python | 992 | 25 | """Session loader dispatch for the stim cohort.
Mouse 1-5 (ICMS92/93/98/100/101) use the standard DataLoader. Mouse 6 (ICMS83)
was acquired on a different rig with a different on-disk layout (separate
key-file format, E:/ drive) so it needs its own loader; both return the same
DataLoader interface (recording, trial_df... |
cb6b2b5f27646253e694295d4c6bd57e75bedd93d308c901e1168f9430c0692e | Python | 992 | 42 | # -*- coding: utf-8 -*-
import pandas as pd
from pyNBS.pyNBS_stability import full_stability_report
from pyNBS.pyNBS_stability import save_all_stability_plots
cc_file = "pynbs_results/YOUR_CC_MATRIX.csv"
cluster_file = "pynbs_results/YOUR_CLUSTER_ASSIGNMENTS.csv"
prefix = "YOUR_PREFIX"
cc_table = pd.read_csv(cc_file... |
cf866d118eb12fbd4cc382232213008de4982cec8a915f060541e9a87cfecd89 | Python | 993 | 34 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 21 13:34:26 2022
@author: walte
"""
import os
import scipy
basename = os.path.join("C:\Denoising","DCCR-Net","variable_maps")
def get_var_map_conf(im):
shape = im.shape
conf_shape = shape[0]
name = os.path.join(basename,str(conf_shape)+'_map'... |
b15d8c55c0b7427ac81160d13774034122fe7d55455a440982f59d21b1a12f3d | Python | 994 | 36 | import nibabel as nib
import pandas as pd
import numpy as np
lookup_df = pd.read_table(snakemake.params.lookup_tsv, index_col="index")
# get indices and names from lookup table
indices = lookup_df.index.to_list()
names = lookup_df.abbreviation.to_list()
hemis = ["L", "R"]
# create the output dataframe
df = pd.DataF... |
1147310b08f85b659f13ac7a752aaaa0997026444a557f0e1fb72ea94002bf9d | Python | 995 | 35 | import pysam
import argparse
def extract_tags(bam_file, output_tsv):
with pysam.AlignmentFile(bam_file, "rb") as bam, open(output_tsv, "w") as out:
out.write("#read_id\tCarcode\tUMI\tscore\tUMI_trusted\n")
for read in bam:
tags = dict(read.tags)
CB = tags.get("CB", "*")
... |
ffa69525f777d6c21de857949f3be1990bb117a1e82babe08cb3319b73e31ad6 | Python | 995 | 31 | # Python02.py
# IJ BAR: https://github.com/tferr/Scripts#scripts
####################################################
# 2. If statements and for loops
####################################################
a,b = 10,20
my_list = [1, 2, 3, 4]
# An if statement: Indentation is critical in python!
if a in my_list:
print "... |
e3ecd94b15c1600ecf79288e9db6d61fbaa13e0bc2360ffde0b089cf087cc694 | Python | 998 | 38 | import os
import numpy as np
import albumentations
from torch.utils.data import Dataset
from taming.data.base import ImagePaths, NumpyPaths, ConcatDatasetWithIndex
class CustomBase(Dataset):
def __init__(self, *args, **kwargs):
super().__init__()
self.data = None
def __len__(self):
r... |
cf9ae05e830580e1a9f1cc3ae968d52181edf1583316d0d38b137fd993fddd43 | Python | 1,004 | 29 | from setuptools import setup, find_packages
def read_requirements(file_name):
with open(file_name, "r") as file:
return [line.strip() for line in file if line.strip()]
setup(
name='hsnn',
version='1.0.0',
author='Brian Gardner',
author_email="b.gardner@surrey.ac.uk",
description='Hier... |
2a11f40c186dc6590364b332a81c1c2a512b3880defdd74e2a06f939ed59e514 | Python | 1,005 | 28 | from __future__ import annotations
import os
import sys
from pathlib import Path
def _bundle_root() -> Path:
return Path(getattr(sys, "_MEIPASS", Path(sys.executable).resolve().parent))
bundle_root = _bundle_root()
pyside_root = bundle_root / "PySide6"
plugin_root = pyside_root / "plugins"
bundled_platforms_di... |
fc0a720a8013ae6a1baa8da041fd2e967a2ffe1c67c7787ac60fd392ea31b87d | Python | 1,008 | 34 | from setuptools import setup, find_packages
with open("README.md", "r", encoding="utf-8") as fh:
long_description = fh.read()
setup(
name="fwi-msnet",
version="1.0.0",
author="CBJ",
author_email="2023080024@yibinu.edu.cn",
description="Forest Fire Risk Prediction Framework",
long_descripti... |
760c259d8764efe536758244c7ee9ffc5dabf2802e45822f801e86f07b0083f0 | Python | 1,009 | 30 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 19 14:19:52 2022
@author: Joseph Vermeil
GlobalConstants.py - state the global constant of CortExplore programs,
to be imported with "import GlobalConstants as gc" and call the constants with
"gc.my_constant_name".
Joseph Vermeil, 2022
This program is free software: yo... |
87af72a57cb16f05278f37ba39ee788fc2a2b7cbbd7ff84c03d0a84271f68741 | Python | 1,009 | 22 | # 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... |
47bbb07abdffff5321b385b90a1aabec58983a2d0a6d4591cc2326fcaddab4a3 | Python | 1,012 | 43 | # -*- coding: utf-8 -*-
"""For testing neuromaps.datasets.annotations functionality."""
import pytest
from neuromaps.datasets import annotations
@pytest.mark.xfail
def test__groupby_match():
"""Test grouping by matching values."""
assert False
@pytest.mark.xfail
def test__match_annot():
"""Test matchi... |
c78f71fc7a5eec24688b3fbf627554cd69cfbed9e9ed8770368a8d1925d36c20 | Python | 1,012 | 31 | from __future__ import annotations
import logging
from pathlib import Path
from typing import Any
def resolve_log_path(settings: dict[str, Any]) -> Path:
log_dir = Path(settings["logging"]["log_dir"])
log_dir.mkdir(parents=True, exist_ok=True)
file_name = settings["logging"].get("file_name", "workflow.lo... |
4ad2c16775e5954331c4ba96b7127e25054f422ed45fa4bae16fa13f6c7c5901 | Python | 1,014 | 36 | from pathlib import Path
import numpy as np
from steinbock import io
from steinbock.utils import matching
class TestMatchingUtils:
def test_match_masks(self):
mask1 = np.array(
[
[1, 1, 0],
[0, 0, 0],
[0, 2, 2],
],
dtype... |
766f95b8321ce37ad9b8ee660d73f380c6e2b09873d7fdaa41170404bd3bb85f | Python | 1,015 | 33 | # Copyright (c) Facebook, Inc. and its affiliates.
from detectron2.layers import ShapeSpec
from detectron2.utils.registry import Registry
from .backbone import Backbone
BACKBONE_REGISTRY = Registry("BACKBONE")
BACKBONE_REGISTRY.__doc__ = """
Registry for backbones, which extract feature maps from images
The register... |
debf1e7c0157c3318ef11a0f4089b694dfd77a1a28f2b7a0bea1e527b80d9e5e | Python | 1,015 | 32 | #! /usr/bin/env python
"""
Convert empty IPython notebook to a sphinx doc page.
"""
import sys
from subprocess import check_call as sh
def convert_nb(nbname, execute=False):
if execute:
# Execute the notebook
sh(["jupyter", "nbconvert", "--to", "notebook",
"--execute", "--inplace", nbname]... |
f8ae4b5c502278fdbb68c61d870ae191402354a87f38a4814e23d2954f6eaf61 | Python | 1,015 | 33 | from functools import partial
from .mask_rcnn_vitdet_b_100ep import (
dataloader,
lr_multiplier,
model,
train,
optimizer,
get_vit_lr_decay_rate,
)
train.init_checkpoint = (
"detectron2://ImageNetPretrained/MAE/mae_pretrain_vit_huge_p14to16.pth?matching_heuristics=True"
)
model.backbone.ne... |
dfea7d3d313a3ce0274bf18532ec18a4bb0e15a3bd964e11204b917e822984aa | Python | 1,021 | 31 | from glob import glob
from pathlib import Path
import subprocess
def calc_distances(genus: str, out_parent: str | Path) -> None:
"""
Parent method for RAxML distance calculation
Args:
genus: The current genus
out_parent: Parent data directory
"""
out_dir = f"{out_parent}/no_interp... |
4280c4a11192bac6d424e1a765832baa9c7abd1f966141476958e89255507d4b | Python | 1,023 | 33 | from functools import partial
from .cascade_mask_rcnn_vitdet_b_100ep import (
dataloader,
lr_multiplier,
model,
train,
optimizer,
get_vit_lr_decay_rate,
)
train.init_checkpoint = (
"detectron2://ImageNetPretrained/MAE/mae_pretrain_vit_huge_p14to16.pth?matching_heuristics=True"
)
model.bac... |
a1e1be9445c27052bcec3eca739ee284ace113db555ebac612c2033f47130b41 | Python | 1,024 | 33 | import collections
from collections import OrderedDict
from pathlib import Path, PosixPath, WindowsPath
from typing import TYPE_CHECKING, Any
if TYPE_CHECKING:
from ruamel.yaml import YAML, Dumper
else:
try:
from ruamel.yaml import YAML, Dumper
except ImportError: # pragma: no cover
from r... |
b86f8c590b0749e3d0ea5747419ef1a6bbeb11af4d89975fcbcf171e96546ec7 | Python | 1,027 | 26 | #https://www.mcponline.org/content/13/12/3497.long#sec-1
from pathlib import Path
pathFiles = Path("L:/promec/Qexactive/LARS/2019/oktober/Kristine Sonja/txt")
fileName='proteinGroups.txt'
trainList=list(pathFiles.rglob(fileName))
import pandas as pd
df=pd.read_csv(trainList[0],low_memory=False,sep='\t')
print(df.head(... |
2dc5d09af8ff343b1698d6a07f946dd3956e7a12268dd6766c1d3fce792af11f | Python | 1,028 | 31 | import shutil
from pathlib import Path
from typing import Generator
import pytest
import requests
_imc_test_data_steinbock_url = (
"https://github.com/BodenmillerGroup/TestData"
"/releases/download/v1.0.7/210308_ImcTestData_steinbock.tar.gz"
)
_imc_test_data_steinbock_dir = "datasets/210308_ImcTestData/steinb... |
f5f460d4d757c1ad12fc195cba898e709378491d701da1bbc569b1315dfd8050 | Python | 1,031 | 25 | from mesa.examples.advanced.alliance_formation.model import MultiLevelAllianceModel
from mesa.examples.advanced.epstein_civil_violence.model import EpsteinCivilViolence
from mesa.examples.advanced.pd_grid.model import PdGrid
from mesa.examples.advanced.sugarscape_g1mt.model import SugarscapeG1mt
from mesa.examples.adva... |
2737125886e0605d7e23901e5cfa9a8e7d34814f11385a4e6e30987893463960 | Python | 1,033 | 36 | # Copyright (c) Facebook, Inc. and its affiliates.
import unittest
from .common import (
get_config_files,
get_evolution_config_files,
get_hrnet_config_files,
get_quick_schedules_config_files,
setup,
)
class TestSetup(unittest.TestCase):
def _test_setup(self, config_file):
setup(conf... |
9a8b277e49c577209ee40461d84ff6d2c57df4e45adb7231ed7619f37b96ea08 | Python | 1,036 | 47 | import math
def uniform(size, tensor):
bound = 1.0 / math.sqrt(size)
if tensor is not None:
tensor.data.uniform_(-bound, bound)
def kaiming_uniform(tensor, fan, a):
if tensor is not None:
bound = math.sqrt(6 / ((1 + a**2) * fan))
tensor.data.uniform_(-bound, bound)
def glorot(t... |
e716af4ff1a9bf4d1fb45a7cdbc68b50da785e2fbef0d128a6dc3ca230eb6bfd | Python | 1,039 | 39 | #
# Copyright (c) 2024 10X Genomics, Inc. All rights reserved.
#
"""Disable reporter stages based on cell annotation outs."""
import csv
from cellranger.cell_typing.common_cell_typing import (
BARCODE_KEY,
COARSE_CELL_TYPES_KEY,
)
__MRO__ = """
stage DISABLE_CAS_REPORTER_STAGES(
in csv cell_types,
... |
316a283d4bf70b5fcd7d167b9e6ea430dadee1cdde1a4d96c9d6d3ed507609cf | Python | 1,045 | 37 | """
Spyne - A Python package for analyzing calcium imaging data from dendrites and spines.
"""
__version__ = "0.1.0"
from .core.imaging.imagingdataset import ImagingDataset
from .core.electrophysiology.ephydataset import EphyDataset
from .core.spines.spinedataset import SpineDataset
# Import plot submodule
from . imp... |
fa24985c4fd66ced9410fad15f2998a056563dbc4b5777fd74cb0dddb81e978c | Python | 1,045 | 37 | from ._ilastik import (
SteinbockIlastikClassificationException,
create_and_save_ilastik_project,
create_ilastik_crop,
create_ilastik_image,
fix_ilastik_project_file_inplace,
list_ilastik_crop_files,
list_ilastik_image_files,
logger,
read_ilastik_crop,
read_ilastik_image,
run... |
7a685d125549ea0f43c1879f01fe6beca01f0ac111c718076d758dc3dd12078a | Python | 1,048 | 32 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
import unittest
import torch
from torch.autograd import gradcheck
from tensormask.layers.swap_align2nat import SwapAlign2Nat
class SwapAlign2NatTest(unittest.TestCase):
@unittest.skipIf(not torch.cuda.is_available(), "CUDA not available")... |
775b99639c717b1df8daf9d9f728e73bb202b8fd6510d3d0f8188372e468d7d2 | Python | 1,053 | 40 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import os
from typing import Dict, Optional
from detectron2.config import CfgNode
def is_relative_local_path(path: str) -> bool:
path_str = os.fsdecode(path)
return ("://" not in path_str) and not os.path.isabs(path)
def maybe_prepend_base_... |
29f22f59ec7637b8c288cef813175f760b29133b31165b3b858987234331d62c | Python | 1,054 | 32 | import shutil
from pathlib import Path
import pytest
from steinbock.segmentation import cellprofiler
cellprofiler_binary = "cellprofiler"
cellprofiler_plugin_dir = "/opt/cellprofiler_plugins"
class TestCellprofilerSegmentation:
def test_create_and_save_segmentation_pipeline(self, tmp_path: Path):
cellp... |
ffc0d0faa341351a1537d70486b4cb10a250cd25e794421cf7667ba5cbd9063c | Python | 1,054 | 64 | # -*- coding: utf-8 -*-
"""For testing neuromaps.nulls.nulls functionality."""
import pytest
@pytest.mark.xfail
def test_alexander_bloch():
"""Test alexander-bloch null model."""
assert False
@pytest.mark.xfail
def test_vasa():
"""Test vasa null model."""
assert False
@pytest.mark.xfail
def test_... |
c12d49f874a1c9b1af61350cd1a9e27fa19a16593be70a133716178423d178fb | Python | 1,056 | 32 | # Copyright (c) Facebook, Inc. and its affiliates.
import cloudpickle
class PicklableWrapper:
"""
Wrap an object to make it more picklable, note that it uses
heavy weight serialization libraries that are slower than pickle.
It's best to use it only on closures (which are usually not picklable).
T... |
62c959c49b7b2b6ff1d17ca2e716138e07e5d8fcc22f35d8e9c364fd66b0c1ef | Python | 1,057 | 29 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
K-mer indexers for fast approximate string matching in b... |
1cae8cfadb9b37f1acd7a8401f513cb38e5ac5c0ab3d3e09a079ff4d27e8649c | Python | 1,059 | 35 | """
Setup module adapted from setuptools code. See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
setup(
name='pyNBS',
version='0.2.0',
description='Python package to perform n... |
3fff008ef5bfbe4861f830af8f62a222562fce6be7461035b11af6d6f767d7ff | Python | 1,059 | 26 | #https://www.tensorflow.org/neural_structured_learning
import tensorflow as tf
import neural_structured_learning as nsl
# Prepare data.
(x_train, y_train), (x_test, y_test) = tf.keras.datasets.mnist.load_data()
x_train, x_test = x_train / 255.0, x_test / 255.0
# Create a base model -- sequential, functional, or subcl... |
9350a15d6c26ec8fb5c72767cdb9dcc466cc588e8d3a98ed45d8963e221c5eeb | Python | 1,059 | 21 | import pandas as pd
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.decomposition import LatentDirichletAllocation
from sklearn.cluster import KMeans
from sklearn.metrics import normalized_mutual_info_score, adjusted_rand_score
def run_topic_pipeline(csv_path, seed=42, n_topics=8, max_features... |
1f37ce3ff87805f29edee384bcffd8fde9c2a02695b0adddd489c1537c9940bd | Python | 1,060 | 49 | import numpy as np
import scipy
import matplotlib.pyplot as plt
from scipy.spatial import Delaunay
import matplotlib
matplotlib.use('Agg')
multires_points = list()
N=128
print(f'N for gridding is: {N}')
nx, ny = (2*N,N)
print(f'nx: {nx}')
print(f'ny: {ny}')
x = np.linspace(0,40, nx)
y = np.linspace(0,20, ny)
print(... |
0fd5689220621dca705fd07d42553ae31a8539e8278bb6a3fa3d7c127b8c0056 | Python | 1,061 | 32 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
from isoquant_lib.common import junctions_from_blocks
def ... |
60cbf34994ca460e25f65bd226764374af05bf555aea6423beee47f0e1d9f465 | Python | 1,062 | 32 | import shutil
from pathlib import Path
import pytest
from steinbock.measurement import cellprofiler
cellprofiler_binary = "cellprofiler"
cellprofiler_plugin_dir = "/opt/cellprofiler_plugins"
class TestCellprofilerMeasurement:
def test_create_and_save_measurement_pipeline(self, tmp_path: Path):
cellprof... |
7191746b68ec57482875af21cd3176a1c73cb1dbc5234ac8c8747d9c74c97cd0 | Python | 1,064 | 45 | from typing import Any
import numpy as np
__all__ = ["pop_attr"]
def pop_attr(o: object, attr: str, *args) -> Any | None:
"""like ``pop()`` but for attribute maps"""
match len(args):
case 0:
return _pop_attr(o, attr)
case 1:
return _pop_attr_d(o, attr, args[0])
... |
b45af4b3e292664118a1773d8adc09a2fdcab10ee856bfe55dd666c492489a80 | Python | 1,066 | 30 | from __future__ import annotations
from src.utils.config import (
load_settings,
merge_settings,
resolve_project_path,
resolve_settings_paths,
)
def test_default_settings_keep_mopac_disabled() -> None:
settings = load_settings()
assert settings["pm7"]["enabled"] is False
def test_output_di... |
0eb7ba95e322dae74b12090a6b624eed0e4f35309d1605130890ac8fdc6365a4 | Python | 1,067 | 36 | '''
This package provides tools for analyzing and classifying calcium imaging data.
It includes modules for data preprocessing, model training, and inference.
'''
from .core.dffdataset import DffDataset
from .core.classifier_dff import CalciumEventClassifierDff
from .core.inference import is_calcium_event, load_classif... |
2318caeda798ec8cc56097fbe4b22402454c333a5aa6544a3f0e553cfbab78e3 | Python | 1,069 | 36 | #
# Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
#
"""Utility for getting the version of the pipeline."""
from __future__ import annotations
import os.path
import tenkit.log_subprocess as tk_subproc
def get_version():
"""Get the version for the pipeline.
Normally it will read this from the... |
3dd0ee793a50e324e7058223211dbcbc12d57a939bd4848b9ddc1e02003fcbd7 | Python | 1,070 | 28 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from contextlib import contextmanager
from openff.toolkit import GLOBAL_TOOLKIT_REGISTRY, OpenEyeToolkitWrapper
from openff.toolkit.utils.toolkit_registry import ToolkitUnavailableException
... |
875d2d0654ccd8014911d416241ba9f6c53701b72a8010fd703eb50d33f20c7f | Python | 1,074 | 44 | '''
Created on 08.04.2019
@author: Niklas Pallast
process all DTI data
'''
import glob
import os
import numpy as np
def findData(path):
regAtlas_list = []
fileALL = glob.iglob(path + '/P*/S*/DTI/DSI_studio/*_rsfMRISplit_scaled.nii.gz', recursive=True)
for filename in fileALL:
regAtlas_list.ap... |
85f02f966fde7ebd7c23fbbb57aa7ad39728cb6e01612f2b9e63c639be70da37 | Python | 1,077 | 47 | """
Created on May 14, 2025.
@author: voodoocode
"""
import pyvista
import numpy as np
import sklearn.cluster
import scipy.ndimage
import shutil
import finnpy.src_rec.utils
import os
np.random.seed(0)
STRUCT_PATH = "/mnt/data/Professional/projects/finnpy/DISTAL (Ewert 2017)/lh/Subthalamic Nucleus.obj"
STRUCT_NAME =... |
6741bb9eae66387678a2ef50f13b0874cff6907ebd305d139e61d4ee3faabde1 | Python | 1,083 | 38 | #
# Copyright (c) 2025 10X Genomics, Inc. All rights reserved.
#
"""Get legacy cell type outs."""
import json
import martian
__MRO__ = """
stage MERGE_ALL_CELL_TYPE_METRICS(
in json cell_annotation_primary_metrics,
in json cell_annotation_analysis_metrics,
out json merged_cell_annotation_metrics,
s... |
27e0c7f22a10d595e6edd75acc9d665f3eec3d49ec862ba7acee1366fe896bf9 | Python | 1,084 | 33 | from pathlib import Path
import scipy.io
from . import config
VAL_ROOT = Path(config["paths"]["val_root"])
VAL_ROOT.parent.mkdir(parents=True, exist_ok=True)
META_PATH = Path(config["paths"]["meta_path"])
META_PATH.parent.mkdir(parents=True, exist_ok=True)
LABEL_FILE = Path(config["paths"]["label_file"])
LABEL_FILE... |
0d8ed4c1c97876b853e8c231786fa24e99a5d3df1679c42c4673012cf7470249 | Python | 1,085 | 35 | import sys
from pathlib import Path
import pandas as pd
SCRIPTS = Path(__file__).resolve().parents[1] / "scripts"
sys.path.insert(0, str(SCRIPTS))
from run_missing_data_sensitivity import compare_screens, select_top
def test_screen_comparison_reports_set_based_top_k_overlap_and_rank_agreement():
left = pd.Dat... |
425ad3577d58a659260c9bbef555a8ae19a638b5905dedb1d6f8632a2ae654e5 | Python | 1,085 | 27 | import shutil
from batchgenerators.utilities.file_and_folder_operations import isdir, join
from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name
from nnunetv2.paths import nnUNet_raw
if __name__ == '__main__':
dataset_name = 'IntegrationTest_Hippocampus'
dataset_id = 999
... |
743af165c77e20e869191039718724e63b609933bf464941555f0afcdf47b2d8 | Python | 1,086 | 30 | #%% imports
import sys
sys.path.append('/mnt/obob/staff/fschmidt/neurogram/cluster_jobs')
from cluster_jobs.stats_across_eog import StatsAcross
from plus_slurm import SingularityJobCluster, PermuteArgument
#% get jobcluster
job_cluster = SingularityJobCluster(required_ram='4G',
request_time=6... |
246b869be24d3c52c5a14fd79695c93c2508a23aa03841726a3d4c774b430590 | Python | 1,088 | 32 | from __future__ import annotations
import importlib.metadata as impm
import re
import jinja2
import requests
from jinja2.ext import Extension
class SnakebidsVersionExtension(Extension):
"""Retrieve the latest snakebids version from pypi.
Stores value in the ``snakebids_version`` global variable.
"""
... |
5e666042d2d45494e4bff780f35312367e6feca795863c54834dca09a4fa1fb1 | Python | 1,089 | 54 | '''
Created on Oct 9, 2025
@author: voodoocode
'''
import numpy as np
def rigid_transform_3D(A, B):
centroid_A = np.mean(A, axis=0)
centroid_B = np.mean(B, axis=0)
AA = A - centroid_A
BB = B - centroid_B
H = AA.T @ BB
# SVD decomposition
U, S, Vt = np.linalg.svd(H)
R = Vt.T @ U.T
... |
33d7f004d9aff5803cddb0395e760848e3f059bf0ae0a933312b7ab74fdf3fb3 | Python | 1,092 | 38 | from collections import OrderedDict
import yaml
from pathlib import Path
import torch
from torchvision import models
from .. import config
def load_model(device):
model_path = Path(config["model_path"])
model = models.resnet50(weights=None).to(device)
checkpoint = torch.load(model_path, map_location=de... |
40cdb8b761afe9847f838c875fbd5e572270b1780dc65718bc030beb8b810975 | Python | 1,095 | 32 | # eeg_visual_classification/models/registry.py
from .EEGNET import Model as EEGNet
from .blstm import Model as blstm
from .BrainDecoder import Model as BrainDecoder
from .NeuroStream import Model as NeuroStream
from .lstm import Model as lstm
from .SleepingPower import Model as SleepingPower
from .EEGChannelNet import ... |
538f8ced9697500ae8bcc2efeada2b1a1298031db655013099cf3aca8231e0aa | Python | 1,099 | 30 | from __future__ import annotations
from typing import Any
from src.tautomer.base import TautomerError, Tautomerizer
def build_tautomerizer(settings: dict[str, Any] | None) -> Tautomerizer | None:
"""Return a tautomer backend, or ``None`` when the step is disabled.
The tautomer step is opt-in (``tautomer.en... |
404b3dfc783f9410acec36a0c22c06efb2e4b65c28a803addc1f8aa04e726704 | Python | 1,100 | 38 | import scanpy as sc
import pandas as pd
import numpy as np
csv_path = "PATH_TO_INPUT_CSV/samap_leiden_clusters.csv"
h5ad_path = "PATH_TO_OUTPUT_DIR/yours.h5ad"
df = pd.read_csv(csv_path)
required_cols = ["X", "leiden", "celltype", "batch"]
for col in required_cols:
if col not in df.columns:
raise ValueEr... |
d93a379ceac94ba6e90c221c34ebedd7c896ef354a994cf83a46f57925100560 | Python | 1,100 | 37 | import os
import pickle
import pandas as pd
import scanpy as sc
pkl_path = "PATH_TO_INPUT/SAMAP_processed.pkl"
output_dir = "PATH_TO_OUTPUT_DIR/SAMap/"
os.makedirs(output_dir, exist_ok=True)
with open(pkl_path, "rb") as f:
sm = pickle.load(f)
adata = sm.samap.adata
adata.obs["batch"] = adata.obs["species"].as... |
a13d5aea2c4dd78acdf61ff4a0dcd4c01833d634d1c8c0d80484c627c0d71b7d | Python | 1,103 | 42 | from typing import Dict, Optional, Sequence
import numpy as np
def view(
img: np.ndarray,
masks: Optional[Dict[str, np.ndarray]] = None,
channel_names: Optional[Sequence[str]] = None,
pixel_size_um: float = 1.0,
run: bool = True,
**viewer_kwargs,
) -> Optional["napari.Viewer"]:
import nap... |
d0b1a0e50eeee2b59244fd4258f458cbd594a4ce886717eca0f6981595f0b348 | Python | 1,103 | 38 | #
# Copyright (c) 2023 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import base64
import struct
def array_to_float32_base64(vals):
"""Convert an array of doubles to a little endian base64 encoded ASCII string.
Args:
vals: a list of float values
Returns:
A... |
5c746ec931cebb509810a961235dc5e312791a07b2d8c06b05e03cbc7dac6bd2 | Python | 1,106 | 40 | #!/usr/bin/env python3
import numpy as np
from typing import List
from detectron2.structures import Instances
def create_prediction_pairs(
instances: Instances,
prev_instances: Instances,
iou_all: np.ndarray,
threshold: float = 0.5,
) -> List:
"""
Args:
instances: predictions from cur... |
8ad018155ba890d782a943cc687099d5796ebfc30fb7bc2d117603d95cc0807f | Python | 1,106 | 54 | """
ROIpy is a package for region of interest (ROI) creation
compatible with ScanImage.
"""
__version__ = "0.1.0"
from .core.structures import Stack, Morphology, Scanfields
from .GUIv2.main import run_app
# Import plot submodule
from .plot.plot import plot, animate
from .analysis import stats
import sys
from pathl... |
4375a6c192a167995c4bc11598f61b4f25f4d3d557d15ffc90353e395943231f | Python | 1,108 | 35 | """Test validation for HexGrid torus configurations."""
import random
import pytest
from mesa.discrete_space import HexGrid
def test_hexgrid_torus_odd_dimensions_error():
"""Test that HexGrid raises ValueError when torus=True and dimensions are odd."""
# Helper to assert error
with pytest.raises(
... |
663da1028ca55a746d68e3291ca95637ef614dbadb2974795bbba3b2489e6a42 | Python | 1,108 | 38 | import scipy.io
import numpy as np
from scipy.spatial import Voronoi
import math
data = scipy.io.loadmat('temp_file.mat')
points = data['points']
def PolyArea(x,y):
return 0.5*np.abs(np.dot(x,np.roll(y,1))-np.dot(y,np.roll(x,1)))
vor = Voronoi(points)
point_to_cell_index = list(vor.point_region)
reg... |
b91e6ef9eed1369b170d52ea8cb5e20b917a0eaa4a6c04e0108400f770642ff4 | Python | 1,108 | 40 | import importlib
import platform
import sys
REQUIRED_RUNTIME = {
"numpy": "numpy",
"pandas": "pandas",
"sklearn": "scikit-learn",
"yaml": "PyYAML",
"joblib": "joblib",
}
OPTIONAL_FULL = {
"torch": "torch",
"transformers": "transformers",
"jieba": "jieba",
}
print("Platform:", platform.... |
5db6fa9b67dd11bc1bbfbd433f0b9552a5832388d012105ad0824556a7a985e7 | Python | 1,110 | 38 | from dataclasses import dataclass, field
from pathlib import Path
from typing import Any
from .. import io
from ._checkpoint import CheckpointView
__all__ = ['TrialView']
@dataclass
class TrialView:
path: Path = field(repr=False)
name: str = field(init=False)
def __post_init__(self):
self.path... |
8c4106c4cf4129d849e55dc6fd37a42f4f1c3521f3f49c79ba513cc08a03aa6a | Python | 1,110 | 34 | import shutil
import uuid
from src.utils.config import PROJECT_ROOT
from src.utils.models import ProtonatedLigandRecord
from src.visualization.structure_panels import StructurePanelGenerator
def test_generate_structure_panel_pdf() -> None:
output_dir = PROJECT_ROOT / "data" / "intermediate" / "test_tmp" / str(uu... |
a3da905c15e75c7b184caa9dd99380114e6b232e9838319e70abb6b33c0b7a25 | Python | 1,110 | 35 | # 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... |
e36b5342549901af664e6f0a61edeb9aa26be47bfb101ff742c701c599a51166 | Python | 1,110 | 33 | import pathlib
import pytest
from click.testing import CliRunner
from openfecli.fetchables import RBFE_TUTORIAL, RBFE_TUTORIAL_RESULTS
from openfecli.fetching import FetchablePlugin
from .conftest import HAS_INTERNET
def fetchable_test(fetchable):
"""Unit test to ensure that a given FetchablePlugin works"""
... |
6ddd4ad7068b4dd9ba31cabefb674a06a3b140f32776a7109119e6a9448ca037 | Python | 1,117 | 23 | # 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... |
f1fcb9efb6a31ee7f0d77998d66631928dc78264018bfc5b71d05c5bd1921b00 | Python | 1,117 | 37 | """Mesa Signals (Observables) package that provides reactive programming capabilities.
This package enables tracking changes to properties and state in Mesa models through a
reactive programming paradigm. It enables building models where components can observe
and react to changes in other components' state.
The pack... |
216adb98dc0721fa8c334c89132ee2b2a8cd141c25173eebb7e74aee7b5b5f5a | Python | 1,118 | 51 | from features import *
from reduceData import *
from joblib import Parallel, delayed
import multiprocessing
#from runClassifiers import *
import time
def mainRun(indexRun) :
numberOfFolds=10
run=indexRun
start_time = time.time()
globalAnt=0.0
globalIndex=0
globalAccuracy=0.0
X, y, biomarkerNames = loadDataset... |
472d1afc834a00f2ffd48d08d208e537c507acaeec1f90c093f375a15b106339 | Python | 1,119 | 33 | # Clipboard_to_Results.py
# IJ BAR: https://github.com/tferr/Scripts#scripts
#
# Imports numeric values copied to the clipboard into the Results table. It is
# now deprecated. It was of utility prior to BAR v1.1.7, when BARs that analyzed
# tabular data could only read values from the main IJ "Results" table. It is
# i... |
b58b806e1f448ff3e01bb9562373300ab6e340c20b62f45c7c2734a68d2c4a3d | Python | 1,119 | 37 | #!/usr/bin/env python
#
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#
"""Chain types used by the VDJ pipeline."""
from __future__ import annotations
import cellranger.vdj.constants as vdj_constants
# Chain types
TR_CHAIN_TYPE = b"TR"
TR_GD_CHAIN_TYPE = b"TR_GD"
IG_CHAIN_TYPE = b"IG"
VDJ_CHAIN_TYPES =... |
4ef5c0e7a01a241731b3dd71efbc6aad7ebab554555a9cfa3f883bf3b4d9b5a0 | Python | 1,120 | 57 | import scanpy as sc
import anndata
import numpy as np
import scipy.sparse as sp
import pandas as pd
import time
import scvi
import os
input_path = 'PATH_TO_INPUT/combined_adata.h5ad'
combined_adata = sc.read_h5ad(input_path)
start_time = time.time()
scvi.model.SCVI.setup_anndata(
combined_adata,
batch_key="... |
76581a5539ad7a48d6989975cdbcd8ab0b0720614c52799b2d16215dc069dcce | Python | 1,120 | 41 |
from pathlib import Path
import flammkuchen as fl
def save_metadata(
metadata: dict,
save_path: str or Path,
overwrite: bool = False
) -> None:
"""
Save the metadata to a .json file for fast loading and inspection.
Parameters
----------
save_path : Path, optional
Path where to... |
20a99c6b5af449cb92adcba5424d4ee1f0a1318f5cd975096ddff761fae433bf | Python | 1,122 | 37 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 7 13:33:47 2022
@author: schmidtfa
"""
#%% imports
from cluster_jobs.preprocess_meg_sbg import Preprocessing
from plus_slurm import JobCluster, PermuteArgument
import pandas as pd
#%% get jobcluster
job_cluster = JobCluster(required_ram='4G',
... |
37b3ee998ab45df94894b9b311fc70c2fb8a86eeeda952530109a6035796a5cc | Python | 1,124 | 28 | from typing import Dict, Sequence, Tuple
import numpy.typing as npt
from brian2.units import hertz
from ._base import StimulusLayer
from ..groups import GroupFactory
from ...definitions import NeuronClass
__all__ = ["PoissonLayer"]
class PoissonLayer(StimulusLayer):
def __init__(self, name: str, group_shapes: ... |
23ac3b7ad3fd1c4797067948def0e4a5bcad1dbe6a564737d3bac3a777014618 | Python | 1,125 | 57 | # -*- coding: utf-8 -*-
"""For testing neuromaps.nulls.spins functionality."""
import numpy as np
import pytest
from neuromaps.nulls import spins
def test_load_spins():
"""Test loading spins."""
rng = np.random.default_rng()
out = rng.integers(1000, size=(100, 100), dtype='int32')
assert out is spin... |
7f13a4b69cb20e502c98aa060d65012b5f8f2ae055eac83f080be88fe37687d9 | Python | 1,125 | 29 | import sys
from pathlib import Path
SCRIPTS = Path(__file__).resolve().parents[1] / "scripts"
sys.path.insert(0, str(SCRIPTS))
from run_model_sensitivity_pipeline import build_task_commands
def test_orchestration_builds_median_mode_and_shap_commands_for_one_split(tmp_path):
commands = build_task_commands(
... |
6f77e0e6e399e6f6c1c87fa3c53e836667401bccead885aa7bdff990a2933a5b | Python | 1,127 | 45 | from copy import deepcopy
import numpy as np
import pandas as pd
import os
import re
from pathlib import Path
def get_project_root() -> Path:
"""Returns project root folder."""
return Path(__file__).parent.parent.parent
def get_folders(root_folder, pattern):
folders_all = os.listdir(root_folder + '/')
... |
ead2994cad205df94a6fa254a0077039f0b815296069964aded68b6bd653983e | Python | 1,127 | 33 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from ..structures import DensePoseChartPredictorOutput, DensePoseEmbeddingPredictorOutput
from . import (
HFlipConverter,
ToChartResultConverter,
ToChartResultConverterWithConfidences,
ToMaskConverter,
densepose_chart_predictor_outpu... |
0fc2802fb7ecf76cbf200307de173954c009e836edb97dc472899d6e856ca8f3 | Python | 1,129 | 33 | # Copyright (c) 2023 10X Genomics, Inc. All rights reserved.
"""Clonotype related functions."""
from collections import Counter
def extract_clonotype_id_from_name(clonotype_name: str):
"""Extract the clonotype id from a clonotype name string."""
return int(clonotype_name.split("clonotype")[1])
def count_c... |
8b1b6e3d2dff659593471b2d2d6f604e4ae7e7fe67eb7d549abaa76db42b89ff | Python | 1,132 | 38 | # -*- coding: utf-8 -*-
"""
Created on Sun Aug 21 13:34:26 2022
@author: walte
"""
import os
import scipy
import platform
if platform.system() == 'Windows':
basename = os.path.join("C:\Denoising","DCCR-Net","variable_maps")
else:
basename = os.path.join("/mnt/c/Denoising/DCCR-Net/","variable_ma... |
3abdf27559d9345550ad014c0432b185f2cd1b71374e99d9f94c2cf69850a7bc | Python | 1,135 | 45 | import scanpy as sc
import anndata
import numpy as np
import scipy.sparse as sp
import pandas as pd
import time
import scvi
import os
input_path = "PATH_TO_INPUT/combined_adata.h5ad"
combined_adata = sc.read_h5ad(input_path)
print("Available obs columns:", list(combined_adata.obs.columns))
start_time = time.time()
s... |
7ad8f60ffe525719552bcc446719f948bb75ed39249fb85203bc68ea65a5e696 | Python | 1,137 | 43 | # Copyright (c) Facebook, Inc. and its affiliates.
import unittest
import torch
from detectron2.structures import BitMasks, Boxes, Instances
from .common import get_model
# TODO(plabatut): Modularize detectron2 tests and re-use
def make_model_inputs(image, instances=None):
if instances is None:
return ... |
df0e5c110c1d5d14eb2073c0ffbc020e5878e6b72dfd54db7323708af048eba3 | Python | 1,138 | 47 | from __future__ import annotations
import textwrap
import warnings
from colorama import Fore, Style
WARN_TEMPLATE = f"""\
{Fore.YELLOW}{Style.BRIGHT}[{{category}}]{Style.NORMAL} {{filename}}:{{lineno}} \
{Fore.RESET}{{line}}
{{message}}
"""
def formatwarning(
message: Warning | str,
category: type[Warning... |
cd3fc0dba636414ae4729296aa02fd364eb376b4f68a30280cd9163d254d10e3 | Python | 1,142 | 39 | #@ImagePlus img
#@Double(label="X radius",value=2.0) xradius
#@Double(label="Y radius",value=2.0) yradius
#@Double(label="Z radius",value=2.0) zradius
# Python06.py
# IJ BAR: https://github.com/tferr/Scripts#scripts
####################################################
# 6. Further examples
############################... |
e9dec95ba75105a478319aae452d676b88d834721d38df4019bd8063d1f21aa9 | Python | 1,143 | 26 | """
Deprecated location. ResEncUNetPlanner moved to
nnunetv2.experiment_planning.experiment_planners.residual_unets.residual_encoder_unet_planners,
where it lives next to the nnUNetPlannerResEncM/L/XL presets that derive from it.
This module used to hold a second, independently maintained copy of the class. Because `-... |
37e34a0771ef72d6fcc1a6d84f2a05e7dadc2e0b220cd899ecce691f9a683d8d | Python | 1,145 | 36 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from typing import Any
from .base import BaseConverter
class HFlipConverter(BaseConverter):
"""
Converts various DensePose predictor outputs to DensePose results.
Each DensePose predictor output type has to register its convertion strateg... |
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