-## 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