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limax are python utilities for working with LiMAx.

Project description

limax logo

limax: python utilities for LiMAx

GitHub Actions CI/CD Status Current PyPI Version Supported Python Versions GNU Lesser General Public License 3 Zenodo DOI Black mypy

limax is a collection of python utilities for working with LiMAx data with source code available from https://github.com/matthiaskoenig/limax.

The project is developed in collaboration by the Humboldt-University Berlin (Matthias König) and the Jena University Hospital (Hans-Michael Tautenhahn).

Features include:

  • Anonymisation of LiMAx raw data files

  • Visualization of LiMAx DOB curves

  • Calculation of AUC, LiMAx values and other pharmacokinetics parameters from LiMAx DOB curves.

If you have any questions or issues please open an issue.

How to cite

Zenodo DOI

Installation

limax is available from pypi and can be installed via:

pip install limax

Best practise is to setup a virtual environment example via conda and install the package. First install anaconda via https://docs.anaconda.com/anaconda/install/index.html. To run the limax tool open a terminal app (e.g. Application -> Utilities -> terminal on MacOS) and create the conda environment

conda create -n limax python=3.10
conda activate limax
(limax) pip install limax --upgrade

Usage

Command line tool

After installation LiMAx analysis can be performed using the limax command line tool

$ limax

────────────────────────────────────────────────────────────────────────────────
💉 LIMAX ANALYSIS 💉
Version 0.2.4 (https://github.com/matthiaskoenig/limax)
Citation https://doi.org/10.5281/zenodo.7382669
────────────────────────────────────────────────────────────────────────────────
Example processing single LiMAx raw file:
    limax -i patient1.csv -o .
Example processing folder with LiMAx raw files:
    limax -i limax_examples -o limax_examples_processed
────────────────────────────────────────────────────────────────────────────────
Required argument '--input' missing.
Usage: commands.py [options]

Options:
  -h, --help            show this help message and exit
  -i INPUT_PATH, --input=INPUT_PATH
                        Path to folder with LiMAx raw files or single LiMAx
                        raw file as '*.csv'.
  -o OUTPUT_DIR, --output_dir=OUTPUT_DIR
                        Path to output folder with processed LiMAx files as
                        '*.json'.
────────────────────────────────────────────────────────────────────────────────

Common problems

On MacOs the terminal app requires permissions to access files, i.e.

PermissionError: [Errno 1] Operation not permitted

This can be solved by changing the permissions of the terminal app via https://stackoverflow.com/questions/58479686/permissionerror-errno-1-operation-not-permitted-after-macos-catalina-update:

  • Go to System Preference->Security and Privacy.

  • On the left side click on Full Disk Access

  • Now click on bottom left lock icon and enter password to make changes, see Label 3

  • Now click on + sign button

  • Browse the terminal app from Application -> Utilities

License

The limax source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

Funding

This project is supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054) and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 “QuaLiPerF (Quantifying Liver Perfusion-Function Relationship in Complex Resection - A Systems Medicine Approach)” by grant number 436883643 and by grant number 465194077 (Priority Programme SPP 2311, Subproject SimLivA).

Develop version

The latest develop version can be installed via:

pip install git+https://github.com/matthiaskoenig/limax.git@develop

Or via cloning the repository and installing via:

git clone https://github.com/matthiaskoenig/limax.git
cd limax
pip install -e .

To install for development use:

pip install -e .[development]

© 2022-2023 Matthias König, Eva Kindler & Hans-Michael Tautenhahn

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