https://github.com/matthiaskoenig/limax
LiMAx tools
https://github.com/matthiaskoenig/limax
Last synced: 4 months ago
JSON representation
LiMAx tools
- Host: GitHub
- URL: https://github.com/matthiaskoenig/limax
- Owner: matthiaskoenig
- License: lgpl-3.0
- Created: 2022-11-15T12:30:11.000Z (over 2 years ago)
- Default Branch: develop
- Last Pushed: 2023-02-02T13:18:19.000Z (over 2 years ago)
- Last Synced: 2024-04-24T05:47:13.373Z (about 1 year ago)
- Language: Python
- Size: 2.7 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.rst
- Contributing: .github/CONTRIBUTING.rst
- License: LICENSE
- Support: .github/SUPPORT.rst
Awesome Lists containing this project
README
.. image:: https://github.com/matthiaskoenig/limax/raw/develop/docs/images/favicon/limax-100x100-300dpi.png
:align: left
:alt: limax logo
limax: python utilities for LiMAx
==============================================================
.. image:: https://github.com/matthiaskoenig/limax/workflows/CI-CD/badge.svg
:target: https://github.com/matthiaskoenig/limax/workflows/CI-CD
:alt: GitHub Actions CI/CD Status
.. image:: https://img.shields.io/pypi/v/limax.svg
:target: https://pypi.org/project/limax/
:alt: Current PyPI Version
.. image:: https://img.shields.io/pypi/pyversions/limax.svg
:target: https://pypi.org/project/limax/
:alt: Supported Python Versions
.. image:: https://img.shields.io/pypi/l/limax.svg
:target: http://opensource.org/licenses/LGPL-3.0
:alt: GNU Lesser General Public License 3
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7382669.svg
:target: https://doi.org/10.5281/zenodo.7382669
:alt: Zenodo DOI
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/ambv/black
:alt: Black
.. image:: http://www.mypy-lang.org/static/mypy_badge.svg
:target: http://mypy-lang.org/
:alt: 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 Leipzig and 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 `__.
Example plot
============
.. image:: https://github.com/matthiaskoenig/limax/raw/develop/src/limax/resources/processed/example_anonym_2022.png
:align: left
:alt: limax logo
How to cite
===========
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7382669.svg
:target: https://doi.org/10.5281/zenodo.7382669
:alt: 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 :code:`limax` command line tool
.. code:: bash
$ limax
────────────────────────────────────────────────────────────────────────────────
💉 LIMAX ANALYSIS 💉
Version 0.4.3 (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.
.. code:: bash
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
=======
* Source Code: `LGPLv3 `__
* Documentation: `CC BY-SA 4.0 `__
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]
© 2022-2024 Matthias König, Eva Kindler, Anton Schnurpel & Hans-Michael Tautenhahn