FAE

FeAture Explorer (FAE), a radiomics (or medical analysis) tool that helps radiologists extract features, preprocess feature matrix, develop machine learning models (Binary Classification & Survival Analysis) with one-click, and evaluate models qualitatively and quantitatively. This project was inspired on the Radiomics, and provides a GUI with convenient process. FAE was initially developed by East China Normal University and Siemens Healthineers Ltd.

If FAE could help in your project, We appreciate that you could cite this work:

Y. Song, J. Zhang, Y. Zhang, Y. Hou, X. Yan, Y. Wang, M. Zhou, Y. Yao, G. Yang. FeAture Explorer (FAE): A tool for developing and comparing radiomics models. PLoS One. 2020. DOI: https://doi.org/10.1371/journal.pone.0237587

Welcome any issues and PR.

Release

The Windows64 version and the Ubuntut 20.04 release could be found Google Drive or SourceForce. A short tutorial video with Chinese version may help.

Installation

git clone https://github.com/salan668/FAE.git
cd FAE
conda create -n fae python=3.11
conda activate fae
pip install -r requirements.txt

Running

python MainFrameCall.py

Generating UI Files

The .py modules corresponding to each .ui file are checked into the repository for convenience, but must be regenerated whenever a .ui file is modified. Use the pyside6-uic tool that ships with PySide6:

pyside6-uic HomeUI/HomePage.ui                    -o HomeUI/HomePage.py
pyside6-uic Feature/GUI/FeatureExtraction.ui      -o Feature/GUI/FeatureExtraction.py
pyside6-uic Feature/GUI/FeatureMerge.ui           -o Feature/GUI/FeatureMerge.py
pyside6-uic Feature/GUI/IccEstimation.ui          -o Feature/GUI/IccEstimation.py
pyside6-uic BC/GUI/Prepare.ui                     -o BC/GUI/Prepare.py
pyside6-uic BC/GUI/Process.ui                     -o BC/GUI/Process.py
pyside6-uic BC/GUI/Visualization.ui               -o BC/GUI/Visualization.py
pyside6-uic BC/GUI/ModelPrediction.ui             -o BC/GUI/ModelPrediction.py
pyside6-uic SA/GUI/Prepare.ui                     -o SA/GUI/Prepare.py
pyside6-uic SA/GUI/Process.ui                     -o SA/GUI/Process.py
pyside6-uic SA/GUI/Visualization.ui               -o SA/GUI/Visualization.py

After regenerating, verify that the generated files import from PySide6 (e.g. from PySide6 import QtCore, QtGui, QtWidgets) before committing.

Project Structure

FAE/
├── MainFrameCall.py          # Application entry point
├── MainFrameCall_opt.py      # Entry point (compatibility mode, disables native dialogs)
├── HomeUI/                   # Main window and navigation hub
│   ├── HomePageForm.py       # Central controller; owns all submodule instances
│   ├── HomePage.ui / .py     # Qt Designer layout and generated code
│   └── VersionConstant.py    # Version number (MAJOR.MINOR.PATCH)
├── Feature/                  # Radiomics feature engineering
│   ├── FileMatcher.py        # Case / image / ROI file matching
│   ├── SeriesMatcher.py      # Series string matching
│   ├── RadiomicsParamsConfig.py
│   └── GUI/                  # Feature extraction, merge, and ICC estimation forms
├── BC/                       # Binary Classification pipeline
│   ├── DataContainer/        # Feature matrix, labels, and case IDs
│   ├── FeatureAnalysis/      # Balance → Normalize → Reduce → Select → Classify → CV
│   ├── Visualization/        # ROC curves, AUC plots, SHAP bar/beeswarm
│   ├── Description/          # PDF report generation
│   ├── HyperParameters/      # Classifier and selector hyperparameter configs (JSON)
│   └── GUI/                  # Preprocessing, model exploration, and visualization forms
├── SA/                       # Survival Analysis pipeline (mirrors BC structure)
│   ├── PipelineManager.py    # SA pipeline orchestrator
│   ├── DataContainer.py
│   └── GUI/                  # Model exploration and visualization forms
├── Plugin/                   # Plugin launcher
│   └── PluginManager.py      # Discovers plugins via config.json, runs via os.system()
├── Utility/                  # Shared utilities (logging, path helpers, radiomics utils)
├── src/                      # Image assets (PNG icons for the UI)
├── Example/                  # Sample data
└── requirements.txt

License

This project is licensed under the Apache 2.0 License

Contributor and Acknowledge List

• Developer:
  • Yang Song
  • Jing Zhang
  • Guang Yang
  • Chengxiu Zhang
  • Xue-xiang Cao
• Tester:
  • Xu Yan
  • Tian-jing Zhang
  • Yi-lai Pei
  • jmtaysom
  • Zhiyong Zhang
  • Yu-dong Zhang
  • Wei Guo