Getting Started

Prerequisites

Strix is powered by Pytorch, MONAI and Ignite.
Strix relies heavily on following packages to make it work. Theoretically, these packages will be automatically installed via pip installation. If not, please manually install them.

  • pytorch

  • tb-nightly

  • click

  • tqdm

  • numpy

  • scipy

  • scikit-image

  • scikit-learn

  • nibabel

  • pytorch-ignite

  • monai_ex

  • utils_cw

Installation

For developers, we suggest you to get a local copy up and install.

git clone https://gitlab.com/ChingRyu/Strix.git
pip install -e ./Strix

For users, you can just install via pip.

pip install git+https://gitlab.com/ChingRyu/Strix.git

More details please refer to install.

Usage

Strix has 7 different commands:

  • strix-train: Main train entry. Use this command for general DL training process.

  • strix-train-from-cfg: Begin a training process from specified configure file, usually used for reproduction.

  • strix-train-and-test: Begin a full training&testing process automatically.

  • strix-test-from-cfg: Begin a testing processing from specified configure file.

  • strix-nni-search: Use NNI for automatic hyper-parameter tuning.

  • strix-check-data: Visualize preprocessed input dataset.

  • strix-gradcam-from-cfg: Gradcam visualization.

Here is a usage example!
_images/usage-example.png

How to use my own dataset & network?

  • If you want use your own dataset, first you need to create a simple python script of a configuration to generate your dataset. For more details, please refer to this readme

  • If you want try your own network, you need to follow this steps to easily register your network to Strix.

  • After preparation, just simply put own dataset/network file into custom folder, and run!

Roadmap

See the open issues for a list of proposed features (and known issues).

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

License

Distributed under the GNU GPL v3.0 License. See LICENSE for more information.

Contact

Chenglong Wang - clwang@phy.ecnu.edu.cn

Project Link: https://gitlab.com/ChingRyu/Strix