CIS 537 Biomedical Image Analysis - Gastounioti/Kontos Project

Make sure you have installed conda. Then you can simply run

./cnn.sh

It will run from data processing till running the model. If you want to do step by step, please see the follwoing instructions.

Run in the following order

python rename.py

python image_processing_7_featmaps.py

python datasets_adpt_7_featmaps.py

We use conda yaml file to configure the enviornment. You can find the shell script here: https://conda.io/miniconda.html

After running shell script, do the following

anaconda 2 :

export PATH=~/anaconda2/bin:$PATH

anaconda 3 :

export PATH=~/anaconda3/bin:$PATH

Then do the following to create and activate the environment

conda env create -f environment.yml

source activate cis537

Then when running python files, they will be in this envrionment.

Note, to exit the environment, simply run

conda deactivate

Simply run

python CIS537_tensorflow.py