KiMoPack 7.13

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

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)

These commands are installing only KiMoPack and the absolutely needed dependencies. However, there are several modules that work better if additional packages are installed. In general one should try to install all packages at the same time. Additional packages that I generally recommend are h5py and tables (for saving files), python-pptx (for saving power point slides) and keyboard (Window only, for interrupting the fits). Quite useful is also nbopen that allows you to double click on the notebook files. nbopen requires an activation at the end.

(leave away keyboard for Linux!) .. code-block:: text

$ pip install KiMoPack h5py tables nbopen python-pptx

(windows) python -m nbopen.install_win (Linux) python3 -m nbopen.install_xdg (MacOS) Clone the repository and run ./osx-install.sh

Upgrade if already installed:

$ pip install --upgrade KiMoPack

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. See the section towards the end of this Readme.

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.

You can try either of these “lazy” oneliners

ipython -c "import KiMoPack; KiMoPack.download_notebooks()"
python -c "import KiMoPack; KiMoPack.download_notebooks()"
python3 -c "import KiMoPack; KiMoPack.download_notebooks()"

If none of these work then 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.

Quickstart summary

• Install Python >3.8 (Anaconda package or similar) Hint: installing with adding to Path makes life a lot simpler

• Install KiMoPack

  minial: pip install KiMoPack better: pip install KiMoPack h5py tables nbopen python-pptx

• Download Notebooks:

  ipython -c “import KiMoPack; KiMoPack.download_all()” Or https://github.com/erdzeichen/KiMoPack

• Start with:

• (Tutorial Folder) KiMoPack_tutorial_0_Introduction.ipynb (Workflow tools) TA_Raw_plotting_and_Simple_Fit.ipynb for your own data

If you have python in the path: go to the folder where your data is, download/copy the notebooks there (Tutorial or Workflow) and type in a console (e.g. windows +r, or the address line) “jupyter notebook” or “jupyter lab” to start working at this location.

Installing into a local environment

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 kimokack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx

Or if you also want make sure to have a later version of python

$ conda create --name kimopack python=3.11 ipython jupyterlab jupyter
$ conda activate kimopack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx

Error: insufficient rights: If one of the installs complains (error) that the user does not has sufficient rights, this installation can be done attaching “–user”

$ conda create --name kimoPack
$ conda activate kimokack
$ pip install KiMoPack h5py tables keyboard nbopen python-pptx --user

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

Citation

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

Links

• Overview talk: I gave a recent overview talk at the LaserLab Europe meeting: https://youtu.be/z9QqVLFWYrs

• 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