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pysfg

A toolkit to help analysing pump probe sfg data.

Install

  • Install Anaconda for python3 64Bit

  • Setup automatic kernel generation example: conda install nb_conda_kernels

  • Download code

    example: git clone https://github.com/deisi/pysfg.git

  • Navigate to the folder where this reademe.md file is located

    example: cd pysfg

  • Setup a conda environment example: conda env create -f environment.yml

  • If you haven't set up the automatic kernel generation above you now need to do it manually with:

    • Activate the environment with: exmple: conda activate sfg
    • Add a kernel to the default jupyterlab environment example: ipython kernel install --user --name=sfg

Folders

  • pysfg

    Tha place of the backend code. This is where data classes, there input and output is defined.

  • scripts

    A collection of user ready scripts. The scripts is what you as the user want to work with. Each script takes a specific configuration.yaml file as input and generates time results in the form of .json files. These .json files can then be used to further data processing.

    • static_spectra.py Script to help analyse static SFG data. I can be used to automatically averade frames, subtract the background and normalize to a reference.
    • timescan.py Script that deals with time stability of data. It basically looks at the integrated Intensity vs measurement time.
    • bleach.py Script to calculate the bleach of a pump-probe sfg measurement.
    • trace.py Uses the result of bleach to generate pump-probe traces.
    • fit_trace.py Uses the result of trace, to fit the trace with e.g. the nummerical solutioin of the four-level-model
    • psshg.py Script to analyse phase-resolve second harmonic data as produced by e.g. Merlin

  • tests

    A folder with a bunch of unittests. Before codechanges are commited. One has to run: python -m unittests discover -s tests and pass all tests.

  • tutorial

    This folder contains a tutorial in the form of a jupyter lab notebook. The tutorial/Tutorial.ipynb notebook explains how to run and configure the scripts The .yaml files in tutorial can be seen as a reference implementation.

Usage

Have a look at ./tutorial/Tutorial.ipynb, the configuration files in tutorial and maybe even browse through the scripts. This should give you an idear of how this should be used.