#! /bin/bash

for dir in $(find ./neuroglancer-scripts-input/meshes/ -mindepth 1 -maxdepth 1 -type d)
do
  output_json={}
  # exclude files that start with `.` e.g. .gitkeep etc
  for f in $(find $dir/meshes/ -type l -o -type f ! -name \\.* )
  do
    pathedname=${f#$dir/meshes/}
    bname=$(basename $f)
    seg_id=$(echo $bname | sed -E -e 's/WHS_SD_rat_atlas_v4_0+//g' -e 's/\.[a-zA-Z]+$//g')
    # echo ${f#$dir/meshes/}
    final=$(echo $output_json | jq -c ". + {\"$pathedname\": { \"format\": \"STL_ASCII\", \"labelIndex\": $seg_id }}")
    output_json=$final
  done
  echo $output_json | jq '.' > $dir/manifest.json
done