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[FrontAlgorithms.git] / appli / CTBronchi / CTBronchi_process.sh

diff --git a/appli/CTBronchi/CTBronchi_process.sh b/appli/CTBronchi/CTBronchi_process.sh
index f22b699ce9c40efc1e692ed0120ac138bc65d958..1f144db7b0bf5948d34222a797825d90d461d0b9 100755 (executable)
--- a/appli/CTBronchi/CTBronchi_process.sh
+++ b/appli/CTBronchi/CTBronchi_process.sh
@@ -1,95 +1,26 @@
 #!/bin/bash
 
-## Command line arguments
-while [[ "$#" -gt 1 ]]; do
-    key="$1"
-    case $key in
-        -input)
-        input="$2"
-        shift
-        ;;
-        -seed)
-        sx="$2"
-        sy="$3"
-        sz="$4"
-        shift
-        ;;
-        -mori)
-        mori="$2"
-        shift
-        ;;
-        -labels)
-        labels="$2"
-        shift
-        ;;
-        -output)
-        output="$2"
-        shift
-        ;;
-        *)
-        # Do nothing
-        ;;
-    esac
-    shift
-done
-if [ -z "$input" ] || [ -z "$sx" ] || [ -z "$sy" ] || [ -z "$sz" ]; then
-    (>&2 echo "Usage: $0 -input input_raw_image -seed x y z [-mori mori_image_dfilename] [-labels labels_image_filename] [-output output_image_filename] [-mori_init_threshold value] [-mori_end_threshold value] [-mori_delta value] [-mori_minimum_threshold value] [-mori_inside_value value] [-mori_outside_value value] [-mori_signal_kernel_size value] [-mori_signal_threshold value] [-mori_signal_influence value] [-label_upper_threshold value] [-label_inside value] [-label_outside value] [-random_walker_beta value]")
-    exit 1
-fi
-if [ -z "$mori_init_threshold" ]; then mori_init_threshold="-1024"; fi
-if [ -z "$mori_end_threshold" ]; then mori_end_threshold="0"; fi
-if [ -z "$mori_delta" ]; then mori_delta="1"; fi
-if [ -z "$mori_minimum_threshold" ]; then mori_minimum_threshold="-850"; fi
-if [ -z "$mori_inside_value" ]; then mori_inside_value="255"; fi
-if [ -z "$mori_outside_value" ]; then mori_outside_value="0"; fi
-if [ -z "$mori_signal_kernel_size" ]; then mori_signal_kernel_size="20"; fi
-if [ -z "$mori_signal_threshold" ]; then mori_signal_threshold="500"; fi
-if [ -z "$mori_signal_influence" ]; then mori_signal_influence="0.5"; fi
-if [ -z "$label_upper_threshold" ]; then label_upper_threshold="-600"; fi
-if [ -z "$label_inside" ]; then label_inside="1"; fi
-if [ -z "$label_outside" ]; then label_outside="2"; fi
-if [ -z "$random_walker_beta" ]; then random_walker_beta="20"; fi
+input=$1
+dir=`dirname $input`
+base=`basename $1 .mhd`_florez-l
+output="$dir/$base"_segmentation.mhd
+mori="$dir/$base"_mori.mhd
+signal="$dir/$base"_mori_signal.txt
+labels="$dir/$base"_labels.mhd
+diff="$dir/$base"_diff.mhd
+seed="$dir"/seed_florez-l.txt
 
-base_name=`dirname $input`/`basename $input .mhd`
-if [ -z "$mori" ]; then
-    mori="$base_name"_mori.mhd
-fi
-signal="$mori"_signal.txt
-if [ -z "$labels" ]; then
-    labels="$base_name"_labels.mhd
-fi
-if [ -z "$output" ]; then
-    output="$base_name"_rw.mhd
-fi
-
-exec_dir=`dirname $0`
-mori_seg=`dirname $0`/fpa_CTBronchi_MoriSegmentation
-mori_lab=`dirname $0`/fpa_CTBronchi_MoriLabelling
-random_walker=`dirname $0`/fpa_CTBronchi_RandomWalker
-
-$mori_seg \
-    $input $mori $signal \
-    $mori_init_threshold \
-    $mori_end_threshold \
-    $mori_delta \
-    $mori_minimum_threshold \
-    $mori_inside_value \
-    $mori_outside_value \
-    $mori_signal_kernel_size \
-    $mori_signal_threshold \
-    $mori_signal_influence \
-    $sx $sy $sz
-
-$mori_lab \
-    $input $mori $labels \
-    $label_upper_threshold \
-    $mori_inside_value \
-    $label_inside \
-    $label_outside
-
-$random_walker \
-    $input $labels $output \
-    $label_inside \
-    $random_walker_beta
+(>&2 echo -n "Processing $input... ")
+echo "************************************************"
+./fpa_CTBronchi_Process \
+    -in $input \
+    -out $output \
+    -seed `cat $seed` \
+    -out_mori $mori \
+    -out_signal $signal \
+    -out_labels $labels \
+    -out_diff $diff
+echo "************************************************"
+(>&2 echo "done.")
 
 ## eof - $RCSfile$