lung_extraction.sh

#!/bin/bash

red='\033[1;31m'
green='\033[1;32m'
reset='\033[0m]' #No Color


input_dir=$1
output_dir=$2

# check if the input directory exists and it is provided
if [ -z "$input_dir" ]; then

  echo -e "${red}Error! Input directory not set${reset}"
  exit 1

elif [ ! -d "$input_dir" ]; then

  echo -e "${red}Error! Input directory not found${reset}"
  exit 1

fi


# check if the output directory exists and it is provided
if [ -z "$output_dir" ]; then

  echo -e "${red}Error! Output directory not set${reset}"
  exit 1

# comment the following lines if
# the output directory could not exist
elif [ ! -d "$output_dir" ]; then

  echo -e "${red}Error! Output directory not found${reset}"
  exit 1

fi



# list all the pickle files into the input directory
input_files=$(ls "$input_dir")
echo "Found ${#input_files[@]} files to process"


# apply the pipeline on the input files

for file in $input_files; do

  printf "* Processing $file ...       "

  f="${file%%.nrrd}"
  python3 -m CTLungSeg.lung_extraction --input="$input_dir$file" --output="$output_dir$f.nrrd"

  if [ "$?" = 0 ]; then
    echo -e "${green}[done]${reset}"
  else
    echo -e "${red}[failed]${reset}"
    exit 1 # you can omit this line if you want to catch
           # possible errors into the log without an exit
  fi

done