CMDS-Experiment-Toolkit

CMDS-Experiment-Toolkit is a MATLAB software package for processing 1D and 2D spectroscopy data from Phasetech QuickControl outputs.

Prerequisites

• MATLAB — the main entry point (AnalysisHub.mlx) is a MATLAB Live Script (.mlx format)
• Signal Processing Toolbox — required for FFT and filtering operations used throughout the toolkit

Setup

1. Add the Backend/ folder tree to the MATLAB path (use Set Path or addpath(genpath('Backend')) from the repository root).
2. Open AnalysisHub.mlx in MATLAB.
3. Update the data and dataworkup directory paths near the top of AnalysisHub.mlx to match the locations on your local machine.

Usage

AnalysisHub.mlx is organized into self-contained sections that can be run individually rather than executing the entire script from start to finish. The typical analysis workflow proceeds as follows:

1. Loading — reads Phasetech QuickControl output files into MATLAB structs via MDSload
2. Signal Generation — computes rephasing/non-rephasing and absorbance signals
3. FFT — applies complex or real FFT along the coherence time axis
4. Plotting — visualizes 2D spectra, frequency-domain maps, and beat signals
5. Fitting — population subtraction, LPSVD fitting, and oscillation-associated spectra (OAS) analysis

Checkpoints: The toolkit includes checkpoint saves so that processed data can be reloaded in a later session without re-running expensive steps from scratch.

Memory: Processing the full sample dataset requires approximately 2 GB of memory.

Directory Structure

CMDS-Experiment-Toolkit/
├── AnalysisHub.mlx              # Main analysis entry point (MATLAB Live Script)
├── CITATION.cff                 # Citation metadata
├── CHANGELOG.md                 # Version history
├── THIRD_PARTY_LICENSES.md      # Third-party attributions
└── Backend/
    ├── Convenience/             # General-purpose utility functions
    ├── FFT/                     # Fourier transform routines
    ├── Fitting/                 # Population fitting, LPSVD, and OAS analysis
    │   └── OAS/                 # Oscillation-Associated Spectra module
    ├── Inpaint_nans/            # Third-party NaN interpolation toolbox
    ├── Loading/                 # Data loading and parameter configuration
    ├── Plotting/                # 2D spectral plotting and visualization
    └── SignalGeneration/        # Signal computation routines

See the README.md in each Backend/ subdirectory for per-function documentation.

Associated Publication (OAS)

The oscillation-associated spectra (OAS) module is described in:

Kirschner, M. S. et al. "Phonon-induced plasmon-exciton coupling changes probed via oscillation-associated spectra." J. Chem. Phys. (2019). https://doi.org/10.1063/1.5116836

Citing This Work

If you use this toolkit, please cite it using the metadata in CITATION.cff.