KiMoPack 7.4.3

A comprehensive package for the analysis of kinetic data.

KiMoPack

KiMoPack is a project for the handling of spectral data measure at multiple time-points. The current design is optimised for the use with optical transient absorption data, but it has been successfully adapted for the use with transient x-ray emission and spectro-electro chemistry data.

It focuses on the main tasks an experimentator has: Loading and shaping of experiments, plotting of experiments, comparing of experiments, analysing experiments with fast and/or advanced fitting routines and saving/exporting/presenting the results.

For typical use a series of juypter notebooks are provided that guide through the a number of different use scenarios, and are suggesting the parameter that are typically set.

Installation

The basis of the program is a module called “plot_func.py” that contains all the necessary functions and classes. We recommend to use a package manager to install the program.

Install using “pip”:

$ pip install KiMoPack

Upgrade if already installed:

$ pip install KiMoPack -U

Install and update using “conda” from the channel erdzeichen:

$ conda install -c erdzeichen kimopack

Hint: the pip version is usually more recent than the conda version The files can also be downloaded from the github directory https://github.com/erdzeichen/KiMoPack or zenodo (see below)

In general it is a good idea to create a local environment to install files in python if you are using python for many tasks. In a local environment only the packages that are needed are installed, which usually avoids that conflicts can appear. It is very easy to do that.

Under Windows: open the anaconda command prompt or power shell (type anaconda under windows start) Under Linuxs: open a console

$ conda create --name KiMoPack
$ conda activate KiMoPack
$ conda install pytables

If you are working with a very old installation it is usually a good idea to also install an updated python

$ conda create --name KiMoPack python=3.10 ipython jupyterlab jupyter
$ conda activate KiMoPack
$ conda install pytables

into this environment KiMoPack can then be installed. We also recommend (optional) to install python-pptx to create power point slides and nbopen (which allows to automatically open a local server) into the environments. If one of the installs complains (error) that the user does not has sufficient rights, this installation can be done attaching “–user” to the following commands

pip install kimopack

pip install python-pptx
pip install nbopen

Finally, while still in the environement, activate nbopen. There are different commands for Windows/Linux/Mac By doing that in the local environment will open and activate the environment. If you left the environement already you can always go back with “conda activate KiMoPack”

python -m nbopen.install_win
python3 -m nbopen.install_xdg
Clone the repository and run ./osx-install.sh

Error: pytables:

in some versions I have been running in a problem with pytables when loading saved data. Using the conda forge version solved this problem for me

conda install -c conda-forge pytables

Best usage

While KiMoPack is a python library, we facilitate its use with Jupyter notebooks. For the typical analysis tasks we have developed a series of Notebooks that guide through the tasks.n These notebooks can be downloaded from https://github.com/erdzeichen/KiMoPack/tree/main/Workflow_tools or by command line.

To do that start any console (under windows e.g. type “cmd” and hit enter). In the console you then start python by typing “python” and hit enter, lastly you import Kimopack and run a function that downloads the files for you by typing “import KiMoPack; KiMoPack.download_all()” This downloads the notebooks and tutorials from github for you. If you instead use “import KiMoPack; KiMoPack.download_notebooks()” then only the workflow tools are downloaded. Please copy one of these notebooks into your data analysis folder and rename them to create a analysis log of your session. For more information please see the publication https://doi.org/10.1021/acs.jpca.2c00907, the tutorial videos, or the tutorial notebooks under https://github.com/erdzeichen/KiMoPack/tree/main/Tutorial_Notebooks_for_local_use.

Citation

We have written and submitted a paper introducing the toolbox under https://doi.org/10.1021/acs.jpca.2c00907

Links

• Publication: https://pubs.acs.org/doi/10.1021/acs.jpca.2c00907

• Documentation: https://kimopack.readthedocs.io/

• PyPI Releases: https://pypi.org/project/KiMoPack/

• Source Code: https://github.com/erdzeichen/KiMoPack

• Issue Tracker: https://github.com/erdzeichen/KiMoPack/issues

• Website: https://www.chemphys.lu.se/research/projects/kimopack/

• Zenodo: https://zenodo.org/badge/latestdoi/400527965

• Tutorial videos: https://www.youtube.com/channel/UCmhiK0P9wXXjs_PJaitx8BQ