Code Snippets#

Helpful snippets for all things LBM python.

CaImAn Parameters#

Troubleshooting#

You may need some additional dependencies on WSL2:

sudo apt-get update && apt-get install ffmpeg libsm6 libxext6  -y

Filepaths and data directories#

def get_files(pathnames: os.PathLike | List[os.PathLike | str]) -> List[PathLike[AnyStr]]:
    """
    Expands a list of pathname patterns to form a sorted list of absolute filenames.

    Parameters
    ----------
    pathnames: os.PathLike
        Pathname(s) or pathname pattern(s) to read.

    Returns
    -------
    List[PathLike[AnyStr]]
        List of absolute filenames.
    """
    pathnames = Path(pathnames).expanduser()  # expand ~ to /home/user
    if not pathnames.exists():
        raise FileNotFoundError(f'Path {pathnames} does not exist as a file or directory.')
    if pathnames.is_file():
        return [pathnames]
    if pathnames.is_dir():
        pathnames = [fpath for fpath in pathnames.glob("*.tif*")]  # matches .tif and .tiff
    return sorted(pathnames, key=path.basename)

`ImportError: attempted relative import with no known parent package`#

This almost always occurs when you try to run a specific script directly without running the python package i.e. python -m path/to/project/ vs python path/to/project/file.py

main python file

The purpose of this file is to tell our python package how to run the code.

You can execute main.py as if it were a python module, fixing the above import errors.

Like so:

`python /home/mbo/repos/scanreader/scanreader/__main__.py`

Equivlent to:

`python -m /home/mbo/repos/scanreader/scanreader/`

System Information#

cloudmesh-cmd5 is a helpful library to view system information.

Install via pip:

pip install cloudmesh-sys

System Information#
Attribute	Value
BUG_REPORT_URL	“https://bugs.launchpad.net/ubuntu/”
DISTRIB_CODENAME	jammy
DISTRIB_DESCRIPTION	“Ubuntu 22.04.4 LTS”
DISTRIB_ID	Ubuntu
DISTRIB_RELEASE	22.04
HOME_URL	“https://www.ubuntu.com/”
ID	ubuntu
ID_LIKE	debian
NAME	“Ubuntu”
PRETTY_NAME	“Ubuntu 22.04.4 LTS”
PRIVACY_POLICY_URL	“https://www.ubuntu.com/legal/terms-and-policies/privacy-policy”
SUPPORT_URL	“https://help.ubuntu.com/”
UBUNTU_CODENAME	jammy
VERSION	“22.04.4 LTS (Jammy Jellyfish)”
VERSION_CODENAME	jammy
VERSION_ID	“22.04”
cpu	13th Gen Intel(R) Core(TM) i9-13900KS
cpu_cores	16
cpu_count	32
cpu_threads	32
date	2024-08-15 15:59:58.462764
frequency	scpufreq(current=3187.198999999998, min=0.0, max=0.0)
mem.active	248.8 MiB
mem.available	56.3 GiB
mem.free	55.7 GiB
mem.inactive	5.8 GiB
mem.percent	10.2 %
mem.total	62.7 GiB
mem.used	5.7 GiB
platform.version	#1 SMP Thu Mar 7 03:22:57 UTC 2024
python	3.11.9
python.pip	24.2
python.version	3.11.9
sys.platform	linux
uname.machine	x86_64
uname.node	RBO-C2
uname.processor	x86_64
uname.release	5.15.150.1-microsoft-standard-WSL2
uname.system	Linux
uname.version	#1 SMP Thu Mar 7 03:22:57 UTC 2024
user	mbo
+———————+——————————————————————————-+

FAQ#

1. Foreward slash or backwards slash#

When in doubt, use a / foreward slash.

This will work for windows C:/Users/ without needing a double backslash using `pathlib.Path() (built into python).

This will automatically return you a Windows Path or a PosixPath.

Filepaths on WSL

Be sure to not confuse your wsl path //$wsl/home/MBO with your windows home path C:/Users/MBO.

Data path inputs#

# this works on any operating system, any filepath structure
data_path = Path().home() / 'Documents' / 'data' / 'high_res'

raw_files = [x for x in data_path.glob(f'*.tif*')]