clbarnes

import asyncio
import datetime as dt
from functools import wraps
from typing import Union
from httpx import AsyncClient

# unless you keep a strong reference to a running task, it can be dropped during execution
# https://docs.python.org/3/library/asyncio-task.html#asyncio.create_task
_background_tasks = set()

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#!/usr/bin/env python3
"""
Transform between networkx v1 and v2+ node_link_data format.
"""

def node_link_data_1_2(
    data: dict, *, source="source", target="target", name="id", key="key", link="links"
):
    """Update the node_link_data in-place for compatibility with networkx v2+.

clbarnes

#!/usr/bin/env python3
"""
Group nodes together in a networkx DiGraph.

Requires networkx.
"""
from typing import Hashable, Any, Callable, Optional
import networkx as nx

clbarnes

#!/usr/bin/env python3
"""Load a list of images in dask."""
from pathlib import Path
import re
from typing import Callable, Iterable, Optional

import dask.array as da
from dask import delayed
import numpy as np

clbarnes

from functools import lru_cache, wraps
from typing import Optional, Callable
from copy import copy, deepcopy


def copy_cache(deep: bool = True, maxsize: Optional[int] = 128, typed: bool = False):
    """Decorator factory wrapping functools.lru_cache, which copies return values.

    Use this for functions with mutable return values.

clbarnes

#!/usr/bin/env python3
"""Module for building pandas DataFrames by row."""
from collections.abc import Sequence, Collection
import typing as tp

import pandas as pd


class DataFrameBuilder:
    def __init__(

clbarnes

#!/bin/sh
set -e
if [ $# -eq 0 ]; then
        >&2 echo "No argument given, using ls"
        exec ls
elif [ -d "$1" ]; then
        >&2 echo "Directory detected, using ls"
        exec ls "$1"
elif [ -f "$1" ]; then
        >&2 echo "File detected, using less"

clbarnes

#!/usr/bin/env python3
"""
Make a `zpool create ...` command for a set of identical disks,
calculating vdev size etc. from the given configuration.
You will need to know the disk model name;
you should be able to identify it from the output of
`lsblk -d -e 7 -o NAME,SIZE,STATE,MODEL`.
"""
import getpass
from argparse import ArgumentParser

clbarnes

#%%
import os
import shutil
from pathlib import Path
import navis
import numpy as np
from scipy.ndimage import binary_fill_holes

# in nm, for converting world coords to voxel indices
resolution = np.array([3.8, 3.8, 50])

clbarnes

#!/usr/bin/env python
"""
Script for (somewhat safely) adding metadata required by BigDataViewer
(and optionally n5-viewer) to multiscale datasets stored in N5 containers.
"""
from dataclasses import dataclass
import json
from pathlib import Path
from argparse import ArgumentParser
import re