process_collections

#!/bin/bash

export neigh_count=0

neigh_size=3
vox_size=0.15
extent=3
neigh_bounds=0.61
cube_size=1.05

input_dir=/data/home/tclose/Data/Fifty_phantoms/
output_dir=/data/home/tclose/Data/Tractography/chunked

for collection_path in `ls $input_dir`; do
  
  extension=${collection_path##*.}

  if [ $extension = "tck" ]; then
    coll_name=${collection_path##*/}
    coll_name=${coll_name%.*}

    echo "--$coll_name--"
  
#    rm -r $output_dir/${coll_name}/vox_${vox_size}
#    mkdir $output_dir/${coll_name}/vox_${vox_size}

#    chunk_strands $input_dir/$collection_path $output_dir/${coll_name}/vox_${vox_size}/cube_${cube_size}.tck -extent $extent -voxel_size $vox_size -map_to_origin -save_separate -half_offset -neigh_bounds $neigh_bounds
    
#    rm -r $output_dir/${coll_name}/vox_${vox_size}/ball_combined
#    mkdir $output_dir/${coll_name}/vox_${vox_size}/ball_combined

    process_neighbourhoods $output_dir/${coll_name}/vox_${vox_size}/cube_${cube_size} $output_dir/${coll_name}/vox_${vox_size}

#   ls $output_dir/${coll_name}/vox_${vox_size}/prepared_strands $output_dir/prepared_strands/${coll_name}.frr

    #combine_strands $output_dir/${coll_name}/vox_${vox_size}/ball_combined $output_dir/ball_combined/${coll_name}.frr

  fi

done


#combine_strands $output_dir/ball_combined/ $output_dir/ball_combined.frr