Bayesian Uncertainty for Quality Assessment of Deep Learning Contours

This repository contains Tensorflow2.4 code for the paper(s)

• Comparing Bayesian Models for Organ Contouring in Headand Neck Radiotherapy

Installation

1. Install Anaconda with python3.7
2. Install git
3. Open a terminal and follow the commands
   • Clone this repository
     • git clone [email protected]:prerakmody/hansegmentation-uncertainty-qa.git
   • Create conda env
     • (Specifically For Windows): conda init powershell (and restart the terminal)
     • (For all plaforms)

     cd hansegmentation-uncertainty-qa
     conda deactivate
     conda create --name hansegmentation-uncertainty-qa python=3.8
     conda activate hansegmentation-uncertainty-qa
     conda develop .  # check for conda.pth file in $ANACONDA_HOME/envs/hansegmentation-uncertainty-qa/lib/python3.8/site-packages
     

   • Install packages

     • Tensorflow (check here for CUDA/cuDNN requirements)

       • (stick to the exact commands)
       • For tensorflow2.4

       conda install -c nvidia cudnn=8.0.0=cuda11.0_0
       pip install tensorflow==2.4
       

       • Check tensorflow installation

       python -c "import tensorflow as tf;print('\n\n\n====================== \n GPU Devices: ',tf.config.list_physical_devices('GPU'), '\n======================')"
       python -c "import tensorflow as tf;print('\n\n\n====================== \n', tf.reduce_sum(tf.random.normal([1000, 1000])), '\n======================' )"
       

         - [unix] upon running either of the above commands, you will see tensorflow searching for library files like libcudart.so, libcublas.so, libcublasLt.so, libcufft.so, libcurand.so, libcusolver.so, libcusparse.so, libcudnn.so in the location `$ANACONDA_HOME/envs/hansegmentation-uncertainty-qa/lib/`
         - [windows] upon running either of the above commands, you will see tensorflow searching for library files like cudart64_110.dll ... and so on in the location `$ANACONDA_HOME\envs\hansegmentation-uncertainty-qa\Library\bin`
       

       • Other tensorflow pacakges

       pip install tensorflow-probability==0.12.1 tensorflow-addons==0.12.1
       

     • Other packages

       pip install scipy seaborn tqdm psutil humanize pynrrd pydicom SimpleITK itk scikit-image
       pip install psutil humanize pynvml
       

Notes

• All the src/train{}.py files are the ones used to train the models as shown in the demo/ folder