.. 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
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.. 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
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limax is a collection of python utilities for working with
LiMAx data with source code available from
`https://github.com/matthiaskoenig/limax <https://github.com/matthiaskoenig/limax>`__.
The project is developed in collaboration by the Humboldt-University Berlin
(`Matthias König <https://livermetabolism.com>`__)
and the Jena University Hospital (`Hans-Michael Tautenhahn <https://www.uniklinikum-jena.de/avc/Team.html>`__).
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 <https://github.com/matthiaskoenig/limax/issues>`__.
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 <https://pypi.python.org/pypi/limax>`__ 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 0.2.4 (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.
.. 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 <http://opensource.org/licenses/LGPL-3.0>`__
* Documentation: `CC BY-SA 4.0 <http://creativecommons.org/licenses/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 <https://qualiperf.de>`__ (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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"description": ".. image:: https://github.com/matthiaskoenig/limax/raw/develop/docs/images/favicon/limax-100x100-300dpi.png\n :align: left\n :alt: limax logo\n\nlimax: python utilities for LiMAx\n==============================================================\n\n.. image:: https://github.com/matthiaskoenig/limax/workflows/CI-CD/badge.svg\n :target: https://github.com/matthiaskoenig/limax/workflows/CI-CD\n :alt: GitHub Actions CI/CD Status\n\n.. image:: https://img.shields.io/pypi/v/limax.svg\n :target: https://pypi.org/project/limax/\n :alt: Current PyPI Version\n\n.. image:: https://img.shields.io/pypi/pyversions/limax.svg\n :target: https://pypi.org/project/limax/\n :alt: Supported Python Versions\n\n.. image:: https://img.shields.io/pypi/l/limax.svg\n :target: http://opensource.org/licenses/LGPL-3.0\n :alt: GNU Lesser General Public License 3\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7382669.svg\n :target: https://doi.org/10.5281/zenodo.7382669\n :alt: Zenodo DOI\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/ambv/black\n :alt: Black\n\n.. image:: http://www.mypy-lang.org/static/mypy_badge.svg\n :target: http://mypy-lang.org/\n :alt: mypy\n\nlimax is a collection of python utilities for working with\nLiMAx data with source code available from \n`https://github.com/matthiaskoenig/limax <https://github.com/matthiaskoenig/limax>`__.\n\nThe project is developed in collaboration by the Humboldt-University Berlin \n(`Matthias K\u00f6nig <https://livermetabolism.com>`__)\nand the Jena University Hospital (`Hans-Michael Tautenhahn <https://www.uniklinikum-jena.de/avc/Team.html>`__).\n\nFeatures include:\n\n- Anonymisation of LiMAx raw data files\n- Visualization of LiMAx DOB curves\n- Calculation of AUC, LiMAx values and other pharmacokinetics parameters from LiMAx DOB curves. \n\nIf you have any questions or issues please `open an issue <https://github.com/matthiaskoenig/limax/issues>`__.\n\nHow to cite\n===========\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7382669.svg\n :target: https://doi.org/10.5281/zenodo.7382669\n :alt: Zenodo DOI\n\nInstallation\n============\n`limax` is available from `pypi <https://pypi.python.org/pypi/limax>`__ and \ncan be installed via:: \n\n pip install limax\n\nBest practise is to setup a virtual environment example via conda and install the package.\nFirst install anaconda via https://docs.anaconda.com/anaconda/install/index.html.\nTo run the limax tool open a terminal app (e.g. Application -> Utilities -> terminal on MacOS) \nand create the conda environment \n\n::\n\n conda create -n limax python=3.10\n conda activate limax\n (limax) pip install limax --upgrade\n\n\n\nUsage\n=====\n\nCommand line tool\n-----------------\n\nAfter installation LiMAx analysis can be performed using the :code:`limax` command line tool\n\n.. code:: bash\n\n $ limax\n \n 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\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n Example processing single LiMAx raw file:\n limax -i patient1.csv -o .\n Example processing folder with LiMAx raw files:\n limax -i limax_examples -o limax_examples_processed\n \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n Required argument '--input' missing.\n Usage: commands.py [options]\n \n Options:\n -h, --help show this help message and exit\n -i INPUT_PATH, --input=INPUT_PATH\n Path to folder with LiMAx raw files or single LiMAx\n raw file as '*.csv'.\n -o OUTPUT_DIR, --output_dir=OUTPUT_DIR\n Path to output folder with processed LiMAx files as\n '*.json'.\n 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