appli/CTBronchi/Process.sh

   1 #!/bin/bash
   2
   3 ## -- Command line options
   4 vesselness_sigma="0.5"
   5 vesselness_alpha1="0.5"
   6 vesselness_alpha2="2"
   7 mori_min_thr="-850"
   8 mori_kernel="20"
   9 mori_signal_thr="100"
  10 mori_signal_influence="0.5"
  11 mori_lower="-1024"
  12 mori_upper="0"
  13 mori_delta="1"
  14 labels_vesselness_thr="5"
  15 labels_upper_thr="-400"
  16 beta="2.5"
  17 epsilon="1e-5"
  18 while [[ "$#" -gt 0 ]]; do
  19     key="$1"
  20     case $key in
  21         -input)
  22         input=`realpath $2`
  23         shift
  24         ;;
  25         -force)
  26         force="1"
  27         ;;
  28         -vesselness_sigma)
  29         vesselness_sigma="$2"
  30         shift
  31         ;;
  32         -vesselness_alpha1)
  33         vesselness_alpha1="$2"
  34         shift
  35         ;;
  36         -vesselness_alpha2)
  37         vesselness_alpha2="$2"
  38         shift
  39         ;;
  40         -mori_min_thr)
  41         mori_min_thr="$2"
  42         shift
  43         ;;
  44         -mori_kernel)
  45         mori_kernel="$2"
  46         shift
  47         ;;
  48         -mori_signal_thr)
  49         mori_signal_thr="$2"
  50         shift
  51         ;;
  52         -mori_signal_influence)
  53         mori_signal_influence="$2"
  54         shift
  55         ;;
  56         -mori_lower)
  57         mori_lower="$2"
  58         shift
  59         ;;
  60         -mori_upper)
  61         mori_upper="$2"
  62         shift
  63         ;;
  64         -mori_delta)
  65         mori_delta="$2"
  66         shift
  67         ;;
  68         -labels_vesselness_thr)
  69         labels_vesselness_thr="$2"
  70         shift
  71         ;;
  72         -labels_upper_thr)
  73         labels_upper_thr="$2"
  74         shift
  75         ;;
  76         -beta)
  77         beta="$2"
  78         shift
  79         ;;
  80         -epsilon)
  81         epsilon="$2"
  82         shift
  83         ;;
  84         -seed)
  85         seed="$2 $3 $4"
  86         shift
  87         shift
  88         shift
  89         ;;
  90         *)
  91         # Do nothing
  92         ;;
  93     esac
  94     shift
  95 done
  96
  97 ## -- Check command line options
  98 if [ -z "$input" ] || [ -z "$seed" ] ; then
  99     (>&2 echo "Usage: $0 -input <file> -seed <x y z> [-force]")
 100     exit 1
 101 fi
 102
 103 base_dir=`dirname $input | xargs realpath`
 104 base_name=$base_dir/`basename $input .mhd`
 105
 106 vesselness=$base_name"_vesselness.mhd"
 107 mori=$base_name"_mori.mhd"
 108 mori_signal=$base_name"_mori_signal.txt"
 109 labels=$base_name"_labels.mhd"
 110 fastrw=$base_name"_fastrw.mhd"
 111 slicerw=$base_name"_slicerw.mhd"
 112
 113 echo "************************************************"
 114 (>&2 echo "Processing $input... ")
 115 echo "Processing $input..."
 116 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
 117     ./fpa_CTBronchi_Vesselness \
 118         -i $input -o $vesselness \
 119         -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
 120 fi
 121
 122 if [ ! -f $mori ] || [ -n "$force" ] ; then
 123     ./fpa_CTBronchi_MoriSegmentation \
 124         -i $input \
 125         -o $mori \
 126         -s $mori_signal \
 127         -p "$seed" \
 128         -t $mori_min_thr \
 129         -k $mori_kernel \
 130         -r $mori_signal_thr \
 131         -f $mori_signal_influence \
 132         -l $mori_lower \
 133         -u $mori_upper \
 134         -d $mori_delta
 135 fi
 136
 137 if [ ! -f $labels ] || [ -n "$force" ] ; then
 138     ./fpa_CTBronchi_MoriLabelling \
 139         -i $input \
 140         -l $mori \
 141         -v $vesselness \
 142         -o $labels \
 143         -a $labels_vesselness_thr \
 144         -u $labels_upper_thr
 145 fi
 146
 147 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
 148     ./fpa_CTBronchi_FastRandomWalker \
 149         -i $input \
 150         -l $labels \
 151         -o $fastrw \
 152         -b $beta \
 153         -e $epsilon
 154 fi
 155
 156 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
 157     ./fpa_CTBronchi_SliceBySliceRandomWalker \
 158         -i $input \
 159         -l $mori \
 160         -v $vesselness \
 161         -o $slicerw \
 162         -t $labels_vesselness_thr \
 163         -b $beta \
 164         -e $epsilon
 165 fi
 166 (>&2 echo "done.")
 167 echo "done."
 168 echo "************************************************"
 169
 170 ## eof - $RCSfile$