face-rhythm
├── notebooks  <- Jupyter notebooks containing the main pipeline and some demos.
|   ├── basic_face_rhythm_notebook.ipynb  <- Main pipeline notebook.
|   └── interactive_set_ROIs_only.ipynb   <- Notebook for setting ROIs only.
|
├── face-rhythm  <- Source code for use in this project.
│   ├── project.py           <- Contains methods for project directory organization and preparation
│   ├── data_importing.py    <- Contains classes for importing data (like videos)
|   ├── rois.py              <- Contains classes for defining regions of interest (ROIs) to analyze
|   ├── point_tracking.py    <- Contains classes for tracking points in videos
|   ├── spectral_analysis.py <- Contains classes for spectral decomposition
|   ├── decomposition.py     <- Contains classes for TCA decomposition
|   ├── utils.py             <- Contains utility functions for face-rhythm
|   ├── visualization.py     <- Contains classes for visualizing data
|   ├── helpers.py           <- Contains general helper functions (non-face-rhythm specific)
|   ├── h5_handling.py       <- Contains classes for handling h5 files
│   └── __init__.py          <- Makes src a Python module    
|
├── setup.py   <- makes project pip installable (pip install -e .) so src can be imported
├── LICENSE    <- License file
├── Makefile   <- Makefile with commands like `make data` or `make train`
├── README.md  <- The top-level README for developers using this project.
├── docs       <- A default Sphinx project; see sphinx-doc.org for details
└── tox.ini    <- tox file with settings for running tox; see tox.readthedocs.io

Project Directory
├── config.yaml           <- Configuration parameters to run each module in the pipeline. Dictionary.
├── run_info.json         <- Output information from each module. Dictionary.
│
├── run_data              <- Output data from each module.
│   ├── Dataset_videos.h5 <- Output data from Dataset_videos class. Contains metadata about the videos.
│   ├── ROIs.h5           <- Output data from ROIs class. Contains ROI masks.
│   ├── PointTracker.h5   <- Output data from PointTracker class. Contains point tracking data.
|   ├── VQT_Analyzer.h5   <- Output data from VQT_Analyzer class. Contains spectral decomposition data.
│   ├── TCA.h5            <- Output data from TCA class. Contains TCA decomposition data.
│   
└── visualizations        <- Output visualizations.
    ├── factors_rearranged_[frequency].png  <- Example of a rearranged factor plot.
    └── point_tracking_demo.avi             <- Example video.