appli/CTBronchi/Process.sh

   1 #!/bin/bash
   2
   3 ## -- Command line options
   4 curr_dir=`dirname $0`
   5 ext="mha"
   6 vesselness_sigma="0.5"
   7 vesselness_alpha1="0.5"
   8 vesselness_alpha2="2"
   9 mori_min_thr="-850"
  10 mori_kernel="20"
  11 mori_signal_thr="100"
  12 mori_signal_influence="0.5"
  13 mori_lower="-1024"
  14 mori_upper="0"
  15 mori_delta="1"
  16 slice_by_slice_vesselness_thr="5"
  17 fast_vesselness_thr="65"
  18 labels_upper_thr="-400"
  19 beta="2.5"
  20 epsilon="1e-5"
  21 while [[ "$#" -gt 0 ]]; do
  22     key="$1"
  23     case $key in
  24         -input)
  25         input=`realpath $2`
  26         shift
  27         ;;
  28         -force)
  29         force="1"
  30         ;;
  31         -vesselness_sigma)
  32         vesselness_sigma="$2"
  33         shift
  34         ;;
  35         -vesselness_alpha1)
  36         vesselness_alpha1="$2"
  37         shift
  38         ;;
  39         -vesselness_alpha2)
  40         vesselness_alpha2="$2"
  41         shift
  42         ;;
  43         -mori_min_thr)
  44         mori_min_thr="$2"
  45         shift
  46         ;;
  47         -mori_kernel)
  48         mori_kernel="$2"
  49         shift
  50         ;;
  51         -mori_signal_thr)
  52         mori_signal_thr="$2"
  53         shift
  54         ;;
  55         -mori_signal_influence)
  56         mori_signal_influence="$2"
  57         shift
  58         ;;
  59         -mori_lower)
  60         mori_lower="$2"
  61         shift
  62         ;;
  63         -mori_upper)
  64         mori_upper="$2"
  65         shift
  66         ;;
  67         -mori_delta)
  68         mori_delta="$2"
  69         shift
  70         ;;
  71         -slicebyslice_vesselness_thr)
  72         slicebyslice_vesselness_thr="$2"
  73         shift
  74         ;;
  75         -fast_vesselness_thr)
  76         fast_vesselness_thr="$2"
  77         shift
  78         ;;
  79         -slice_by_slice_vesselness_thr)
  80         slice_by_slice_vesselness_thr="$2"
  81         shift
  82         ;;
  83         -labels_upper_thr)
  84         labels_upper_thr="$2"
  85         shift
  86         ;;
  87         -beta)
  88         beta="$2"
  89         shift
  90         ;;
  91         -epsilon)
  92         epsilon="$2"
  93         shift
  94         ;;
  95         -seed)
  96         seed="$2 $3 $4"
  97         shift
  98         shift
  99         shift
 100         ;;
 101         *)
 102         # Do nothing
 103         ;;
 104     esac
 105     shift
 106 done
 107
 108 ## -- Check command line options
 109 if [ -z "$input" ] || [ -z "$seed" ] ; then
 110     (>&2 echo "Usage: $0 -input <file> -seed <x y z> [-force]")
 111     exit 1
 112 fi
 113
 114 base_dir=`dirname $input | xargs realpath`
 115 base_name=$base_dir/`basename $input .$ext`
 116
 117 vesselness=$base_name"_vesselness.$ext"
 118 mori=$base_name"_mori.$ext"
 119 mori_signal=$base_name"_mori_signal.txt"
 120 labels=$base_name"_labels.$ext"
 121 fastrw=$base_name"_fastrw.$ext"
 122 slicerw=$base_name"_slicerw.$ext"
 123 skeleton_fastrw=$base_name"_fastrw_skeleton.txt"
 124 skeleton_slicerw=$base_name"_slicerw_skeleton.txt"
 125 fastrw_points=$base_name"_fastrw_points.txt"
 126 slicerw_points=$base_name"_slicerw_points.txt"
 127
 128 echo "************************************************"
 129 (>&2 echo "Processing $input... ")
 130 echo "Processing $input..."
 131 if [ ! -f $vesselness ] || [ -n "$force" ] ; then
 132     $curr_dir/fpa_CTBronchi_Vesselness \
 133         -i $input -o $vesselness \
 134         -s $vesselness_sigma -a $vesselness_alpha1 -b $vesselness_alpha2
 135 fi
 136
 137 if [ ! -f $mori ] || [ -n "$force" ] ; then
 138     $curr_dir/fpa_CTBronchi_MoriSegmentation \
 139         -i $input \
 140         -o $mori \
 141         -s $mori_signal \
 142         -p "$seed" \
 143         -t $mori_min_thr \
 144         -k $mori_kernel \
 145         -r $mori_signal_thr \
 146         -f $mori_signal_influence \
 147         -l $mori_lower \
 148         -u $mori_upper \
 149         -d $mori_delta
 150 fi
 151
 152 if [ ! -f $labels ] || [ -n "$force" ] ; then
 153     $curr_dir/fpa_CTBronchi_MoriLabelling \
 154         -i $input \
 155         -l $mori \
 156         -v $vesselness \
 157         -o $labels \
 158         -a $fast_vesselness_thr \
 159         -u $labels_upper_thr
 160 fi
 161
 162 if [ ! -f $fastrw ] || [ -n "$force" ] ; then
 163     $curr_dir/fpa_CTBronchi_FastRandomWalker \
 164         -i $input \
 165         -l $labels \
 166         -o $fastrw \
 167         -b $beta \
 168         -e $epsilon
 169 fi
 170
 171 if [ ! -f $slicerw ] || [ -n "$force" ] ; then
 172     $curr_dir/fpa_CTBronchi_SliceBySliceRandomWalker \
 173         -i $input \
 174         -l $mori \
 175         -v $vesselness \
 176         -o $slicerw \
 177         -t $slice_by_slice_vesselness_thr \
 178         -b $beta \
 179         -e $epsilon
 180 fi
 181
 182 if [ ! -f $skeleton_slicerw ] || [ -n "$force" ] ; then
 183     $curr_dir/fpa_CTBronchi_Skeleton \
 184         -i $slicerw \
 185         -o $skeleton_slicerw \
 186         -e $slicerw_points \
 187         -p "$seed"
 188 fi
 189
 190 # if [ ! -f $skeleton_fastrw ] || [ -n "$force" ] ; then
 191 #     $curr_dir/fpa_CTBronchi_Skeleton \
 192 #         -i $fastrw \
 193 #         -o $skeleton_fastrw \
 194 #         -e $fastrw_points \
 195 #         -p "$seed"
 196 # fi
 197 (>&2 echo "done.")
 198 echo "done."
 199 echo "************************************************"
 200
 201 ## eof - $RCSfile$