appli/CTBronchi/CTBronchi_process.sh

   1 #!/bin/bash
   2
   3 ## Command line arguments
   4 if [ "$#" -lt 5 ]; then
   5     echo "Usage: $0 input_image [index/point] seed_x seed_y seed_z"
   6     exit 1
   7 fi
   8
   9 exec_dir=`dirname $0`
  10 mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
  11 mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
  12 random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
  13 input_image=$1
  14 seed_type=$2
  15 seed_x=$3
  16 seed_y=$4
  17 seed_z=$5
  18
  19 base_name=`dirname $input_image`/`basename $input_image .mhd`
  20
  21 mori_output_image="$base_name"_mori.mhd
  22 mori_output_signal="$base_name"_mori_signal.txt
  23 mori_init_threshold=-1024
  24 mori_end_threshold=0
  25 mori_delta=1
  26 mori_minimum_threshold=-850
  27 mori_inside_value=255
  28 mori_outside_value=0
  29 mori_signal_kernel_size=20
  30 mori_signal_threshold=500
  31 mori_signal_influence=500
  32
  33 labels_output_image="$base_name"_labels.mhd
  34 label_upper_threshold=-600
  35 label_inside=1
  36 label_outside=2
  37
  38 random_walker_output_image="$base_name"_rw.mhd
  39 random_walker_alpha=0
  40 random_walker_beta=20
  41
  42 $mori_seg \
  43     $input_image $mori_output_image $mori_output_signal \
  44     $mori_init_threshold \
  45     $mori_end_threshold \
  46     $mori_delta \
  47     $mori_minimum_threshold \
  48     $mori_inside_value \
  49     $mori_outside_value \
  50     $mori_signal_kernel_size \
  51     $mori_signal_threshold \
  52     $mori_signal_influence \
  53     $seed_type \
  54     $seed_x $seed_y $seed_z
  55
  56 $mori_lab \
  57     $input_image $mori_output_image $labels_output_image \
  58     $label_upper_threshold \
  59     $mori_inside_value \
  60     $label_inside \
  61     $label_outside
  62
  63 $random_walker \
  64     $input_image $labels_output_image $random_walker_output_image \
  65     $label_inside \
  66     $random_walker_alpha \
  67     $random_walker_beta
  68
  69 ## eof - $RCSfile$