Covid-19-Pneumonia

Pneumonia segmentation model for CT scans. To be used in the context of covid-19 studies.

Setup: instructions for getting setup on the prp-gpu-1.t2.ucsd.edu machine

0. If you are instead on the AiDA-2 machine, replace each instance below of /xilinx/scratch/software/miniconda3/ with /home/miniconda/miniconda3/

1. Add the following lines to ~/.bashrc:

   # >>> conda initialize >>>
   # !! Contents within this block are managed by 'conda init' !!
   __conda_setup="$('/xilinx/scratch/software/miniconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
   if [ $? -eq 0 ]; then
   eval "$__conda_setup"
   else
   if [ -f "/xilinx/scratch/software/miniconda3/etc/profile.d/conda.sh" ]; then
       . "/xilinx/scratch/software/miniconda3/etc/profile.d/conda.sh"
   else
       export PATH="/xilinx/scratch/software/miniconda3/bin:$PATH"
   fi
   fi
   unset __conda_setup
   # <<< conda initialize <<<

2. mkdir ~/.conda

3. Create a file ~/.conda/environments.txt and add these lines:

   /xilinx/scratch/software/miniconda3
   /xilinx/scratch/software/miniconda3/envs/tensorflow

4. source ~/.bashrc

5. conda activate tensorflow