KinetiKit

INSTALLATION INSTRUCTIONS:

The latest releases of this package can be found on PyPI: https://pypi.org/project/KinetiKit/. An Anaconda Python installation is recommended: https://www.anaconda.com/distribution/ Open the Anaconda Command Prompt and run pip install KinetiKit. To update to the latest version if you have already installed the package, run pip install KinetiKit -upgrade instead.

After installing the package, the simplest way to get started with the program is to come back to this Github page and download some of the files in the examples folder. By saving one of those files as a .py or .ipynb file in a directory that contains your experimental data, you can define file paths in the scripts relative to the path of the scripts themselves.

LIST OF EXAMPLE FILES

• calling_a_custom_model
• custom_models
• FitRates_Biexp
• FitRates_Hetero
• FitRates_Mono
• FitRates_Multipower
• FitRates_shorterTime
• imageShow
• plotTRPL3scales
• pulseViewer
• simplePlotPL
• simplePlotTRPL
• VisualizeSteadyState

In addition, a few iPython notebook files are available for interactive fitting:

• InteractivePlotting_Hetero
• InteractivePlotting_Mono
• InteractivePlotting_Multiexp

QUICK NOTES FOR NON-PYTHONIC FOLKS:

• Note on File paths: If dir_path = os.path.dirname(os.path.realpath(__file__)), then all file paths will be read relative to where this file is located. Alternatively, you can set a directory path as it "normally" appears, e.g. dir_path= r'C:\Users\Me\Documents\MyData'. In general, you can combine paths together (e.g. a path, a subfolder (or multiple subfolders) and a file name by using the command os.path.join(path1, path2, path3...).
• Note on Units: Many units and a few constants have been pre-defined in this package, inside KinetiKit.units. On the provided example files, only the units that are used are imported. If you frequently use a unit that is not already imported, you can add it to the imported list at the top of the file (e.g. from units import ps, fs, MHz).
• Note on Setting and Fitting parameters: As long as bounds have been set for a parameter, its value given in initparams does NOT affect the Differential Evolution search. Parameters for which bounds are not defined will be fixed at the value given in initparams.