SCALP (Skin Cancer Classification Platform)

Project Description

Please refer to

Requirements

• Python 3.6 (3.5+ should work) You can install dependencies with: pip install -r python_requirements.txt
python_requirements_extras.txt contain additional dependencies, used for CNN training and other procedures.

• PostgresSQL 10+ You need to create bbd user and database with bbd owner. You can specify bbd user's password in config.py file. Database dump will be transfered to psql during initial flask server run.

Downloading the data

ISIC Archive Downloader

Example usage:

python ../ISIC-Archive-Downloader/download_archive.py --num-images 1000 -s --images-dir data/ISIC/benign/images --descs-dir data/ISIC/benign/description --seg-dir data/ISIC/benign/segmentation --seg-skill expert --filter benign --p 100
python ../ISIC-Archive-Downloader/download_archive.py --num-images 1000 -s --images-dir data/ISIC/malignant/images --descs-dir data/ISIC/malignant/description --seg-dir data/ISIC/malignant/segmentation --seg-skill expert --filter malignant --p 100

By default Data should be located in src/app/static/ISIC. If you decide to choose other path, you should change it in both db/dump.sql and config.py files.

Trubleshooting

Model hdf5 file missing

If models/CNN_binary_v1.h5 size is <100MB you need to run:

git lfs fetch
git lfs pull