20210927-waxholm-v4/code/run-neuroglancer-script.sh

#! /bin/bash

# convert images

mkdir -p ./output/precomputed/

for f in $(find ./neuroglancer-scripts-input/images -iname "*.nii.gz" -o -iname "*.nii")
do
  filename=${f#./neuroglancer-scripts-input/images/}
  filename_no_ext=${filename%.gz}
  filename_no_ext=${filename_no_ext%.nii}

  outputdir=./output/precomputed/images/$filename_no_ext
  mkdir -p $outputdir
  
  volume-to-precomputed \
    --generate-info \
    $f \
    $outputdir/
  
  generate-scales-info \
    $outputdir/info_fullres.json \
    $outputdir/

  volume-to-precomputed $f $outputdir/

  compute-scales $outputdir/
done

# throw if datatype is not int
for f in $(find ./neuroglancer-scripts-input/segmentations -iname "*.nii.gz" -o -iname "*.nii")
do
  filename=${f#./neuroglancer-scripts-input/segmentations/}
  filename_no_ext=${filename%.gz}
  filename_no_ext=${filename_no_ext%.nii}

  outputdir=./output/precomputed/segmentations/$filename_no_ext
  mkdir -p $outputdir
  
  volume-to-precomputed \
    --generate-info \
    $f \
    $outputdir/
  
  tmp=$(jq -c '. + {"data_type": "uint32"}' $outputdir/info_fullres.json)
  echo $tmp > $outputdir/info_fullres.json

  generate-scales-info \
    --type=segmentation \
    --encoding=compressed_segmentation \
    $outputdir/info_fullres.json \
    $outputdir/

  volume-to-precomputed $f $outputdir/

  compute-scales \
    --downscaling-method=majority \
    $outputdir/
done