20210927-waxholm-v4/code/run-mesh.sh

#! /bin/bash

path_to_gong="./thirdparty/gong-refs.tags.v1.3.0"
output_dir="./output/precomputed/segmentations"

mesh_subdir="meshes"

for dir in $(find ./neuroglancer-scripts-input/meshes/ -mindepth 1 -maxdepth 1 -type d)
do
  cleaned_dir=${dir#./neuroglancer-scripts-input/meshes/}

  root_path=$output_dir/$cleaned_dir/
  info_path=$root_path/info
  mesh_subdir_path=$root_path/$mesh_subdir

  x_transl=$(jq '.[0][3]' $root_path/transform.json)
  y_transl=$(jq '.[1][3]' $root_path/transform.json)
  z_transl=$(jq '.[2][3]' $root_path/transform.json)

  # this looks weird
  # we will cross this bridge when we cross it... 
  x_transl=${x_transl#-}
  y_transl=${y_transl#-}
  z_transl=${z_transl#-}
  base_xform="1e6,0,0,$x_transl,0,1e6,0,$y_transl,0,0,1e6,$z_transl"

  mkdir -p $mesh_subdir_path
  
  [ -f $info_path ] || echo "info $info_path does not exist. Skipping $cleaned_dir"
  [ -f $info_path ] || continue

  for key in $(jq -r 'keys[]' $dir/manifest.json)
  do
    echo Processing $key

    mesh_path=$dir/meshes/$key
    format=$(jq -r ".[\"$key\"].format" $dir/manifest.json)
    seg_id=$(jq -r ".[\"$key\"].labelIndex" $dir/manifest.json)
    new_mesh_name=${key##*/}
    new_mesh_name=${new_mesh_name%.*}

    # convert mesh
    $path_to_gong \
      -outputFormat NG_MESH \
      -dst $mesh_subdir_path/$new_mesh_name \
      -src $mesh_path \
      -srcFormat $format \
      -xformMatrix $base_xform
    
    # add mesh metadata
    mesh_meta_path=$mesh_subdir_path/$seg_id:0
    new_fragments="[\"$new_mesh_name\"]"
    if [ -f $mesh_meta_path ]
    then
      new_mesh_meta=$(jq "{ \"fragments\": (.fragments + $new_fragments) }" $mesh_meta_path)
    else
      new_mesh_meta="{\"fragments\": $new_fragments}"
    fi
    echo $new_mesh_meta | jq -c '.' > $mesh_meta_path
  done

  new_info=$(jq ". + {\"mesh\":\"$mesh_subdir\"}" $info_path)
  echo $new_info | jq -c '.' > $info_path
done