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MAXIE - Masked X-Ray Image AutoEncoder

PyTorch

Config: Hydra

Description

MAXIE contains machinery to build, train, and run AI that operates on masked X-ray images.

Installation

Pip

# clone project
git clone https://github.com/carbonscott/maxie
cd maxie

# [OPTION 1] create python virtual environment
python3 -m venv ./myenv
. ./myenv/bin/activate
export PIP_CACHE_DIR=/tmp/$USER

# [OPTION 2] create conda environment
conda create -n myenv python=3.11
conda activate myenv

# install pytorch according to instructions
# https://pytorch.org/get-started/

# install mpi4py and h5py
MPICC="cc -shared" pip install --no-cache-dir --no-binary=mpi4py mpi4py
HDF5_MPI="ON" CC=cc HDF5_DIR=${HDF5_ROOT} pip install --no-cache-dir --no-binary=h5py h5py

# install requirements
pip install -r requirements.txt

# install maxie (-e for editable install)
pip install -e .

How to run

Train model with default configuration

# train on CPU
python src/train.py trainer=cpu

# train on GPU
python src/train.py trainer=gpu

Train model with chosen experiment configuration from configs/experiment/

python src/train.py experiment=experiment_name.yaml

You can override any parameter from command line like this

python src/train.py trainer.max_epochs=20 data.batch_size=64

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Masked Autoencoder for X-ray Image Encoding (MAXIE)

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