...

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

diff --git a/appli/CTBronchi/CTBronchi_process.sh b/appli/CTBronchi/CTBronchi_process.sh
index 15bd591fbec02d00802ef15c89f5ab856337a584..1f144db7b0bf5948d34222a797825d90d461d0b9 100755 (executable)
--- a/appli/CTBronchi/CTBronchi_process.sh
+++ b/appli/CTBronchi/CTBronchi_process.sh
@@ -1,69 +1,26 @@
 #!/bin/bash
 
-## Command line arguments
-if [ "$#" -lt 5 ]; then
-    echo "Usage: $0 input_image [index/point] seed_x seed_y seed_z"
-    exit 1
-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
-input_image=$1
-seed_type=$2
-seed_x=$3
-seed_y=$4
-seed_z=$5
-
-base_name=`dirname $input_image`/`basename $input_image .mhd`
-
-mori_output_image="$base_name"_mori.mhd
-mori_output_signal="$base_name"_mori_signal.txt
-mori_init_threshold=-1024
-mori_end_threshold=0
-mori_delta=1
-mori_minimum_threshold=-850
-mori_inside_value=255
-mori_outside_value=0
-mori_signal_kernel_size=20
-mori_signal_threshold=500
-mori_signal_influence=500
-
-labels_output_image="$base_name"_labels.mhd
-label_upper_threshold=-600
-label_inside=1
-label_outside=2
-
-random_walker_output_image="$base_name"_rw.mhd
-random_walker_alpha=0
-random_walker_beta=20
-
-$mori_seg \
-    $input_image $mori_output_image $mori_output_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 \
-    $seed_type \
-    $seed_x $seed_y $seed_z
-
-$mori_lab \
-    $input_image $mori_output_image $labels_output_image \
-    $label_upper_threshold \
-    $mori_inside_value \
-    $label_inside \
-    $label_outside
-
-$random_walker \
-    $input_image $labels_output_image $random_walker_output_image \
-    $label_inside \
-    $random_walker_alpha \
-    $random_walker_beta
+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
+
+(>&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 - $RCSfile$