added test script without docker

dice_score_local.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+
+	SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
+	computed=${1}
+	groud_truth=${2}
+	output=$3
+	if [ $# -lt 1 ]; then												
+		echo $0: "usage: "$( basename $0 )" <segmentation1.ext> <segmentation2.ext> [<output>]"
+		return 1;		    
+	fi 
+
+
+
+
+
+if  ! ( [ -z "${computed}" ]  || [  "${computed}" == "null" ] || [ -z "${groud_truth}" ]  || [  "${groud_truth}" == "null" ]   ); then
+
+	echo "computed: "${computed}
+	echo "groud_truth: "${groud_truth}
+
+	inputidr=$( dirname ${computed} )
+
+	[ -z ${output} ] && { output=${inputidr}"/dice_score.txt" ; }
+
+
+	python   ${SCRIPT_DIR}/dice_score.py  ${computed} ${groud_truth} ${output}	
+
+
+
+
+fi

download_testset.sh

@@ -1,6 +1,9 @@
 #! /bin/bash
 tag_list=( ACC PFM MCDs HD )
 #pub_id=$1
+output_dir=./'DBB_test'
+mkdir -p ${output_dir}
 for tag in ${tag_list[@]}; do
-	bl bids download --pub "61b8b6b57ebe1c6fd7f048f2" --tag EMEDEA-PED --tag ${tag} #--output ./DBB_test
+	mkdir -p ${output_dir}'/'${tag}
+	bl bids download --pub "61b8b6b57ebe1c6fd7f048f2" --tag EMEDEA-PED --tag ${tag} --output ${output_dir}'/'${tag}
 done

main_local.sh

@@ -0,0 +1,30 @@
+#! /bin/bash
+	SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
+	t1=$1
+	mask=$2
+	outputdir=$3
+	if [ $# -lt 2 ]; then												
+		echo $0: "usage: "$( basename $0 )" <t1.ext> <mask.ext> [<outputdir>]"
+		exit -1;		    
+	fi 
+
+	echo "t1: "${t1}
+	echo "mask: "${mask}
+	input_dir=$( dirname ${t1} )
+	[ -z ${outputdir} ] && { outputdir=${input_dir}"/segmentation" ; }
+	echo "outputdir: "${outputdir}
+
+	mkdir -p ${outputdir}
+	output=${outputdir}'/segmentation.nii.gz'
+	proc_dir=${input_dir}"/proc/"
+	mkdir -p ${proc_dir}
+	reference=${SCRIPT_DIR}'/data/IMAGE_0426.nii.gz'
+
+	t1_hm=${proc_dir}'/t1_hm.nii.gz'
+	ImageMath 3 ${t1_hm}  HistogramMatch ${t1} ${reference}  
+
+	chkcp_dir=${SCRIPT_DIR}
+
+	python  ${SCRIPT_DIR}/predict.py  ${t1_hm} ${output} ${chkcp_dir} --mask ${mask}
+
+	cp ${SCRIPT_DIR}'/data/label.json' ${outputdir}

predict_testset_local.sh

@@ -0,0 +1,45 @@
+#! /bin/bash
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
+testset_dir=$1
+output_dir=$2
+if [ $# -lt 1 ]; then												
+		echo $0: "usage: "$( basename $0 )" <test_set_dir> [<output_dir>]"
+		return 1;		    
+fi 
+predict_script=${SCRIPT_DIR}/"main_local.sh"
+disce_score_script=${SCRIPT_DIR}/"dice_score_local.sh"
+[ -z ${output_dir} ] && { output_dir=${testset_dir}'/bids/derivatives/bl_app_dbb_DisSeg/' ; }
+mkdir -p ${output_dir}
+for i in $( ls ${testset_dir}/* -d ); do
+	b_name_i=$( basename ${i} )
+	[ "${b_name_i}" == "bids" ] && { continue; }
+	[ -d ${i} ] || { continue; }
+	echo ${i}
+	t1_i=$( ls ${i}'/dt-neuro-anat-t1w.id-'*/'t1.nii.gz' )
+	mask_i=$( ls ${i}'/dt-neuro-mask.id-'*/'mask.nii.gz' )
+	parc_i=$( ls ${i}'/dt-neuro-parcellation-volume.id-'*/'parc.nii.gz' )
+	echo 't1': ${t1_i}
+	echo 'mask': ${mask_i}
+	echo 'parc': ${parc_i}
+	output_dir_i=${output_dir}'/'$( basename ${i}  )'/'
+	echo ${output_dir_i}
+	mkdir -p ${output_dir_i}
+	bash ${predict_script} ${t1_i} ${mask_i} ${output_dir_i}'/'
+	output_seg=${output_dir_i}'/segmentation.nii.gz'	
+	dice_score=${output_dir_i}'/dice_score.txt'
+	bash ${disce_score_script} ${output_seg} ${parc_i} ${dice_score}
+	cat ${dice_score}
+done
+
+csv_file=${output_dir}'/dice_score.csv'
+
+echo "Subject_Id CSF GM WM DGM Brainstem Cerebellum"
+
+echo "Subject_Id CSF GM WM DGM Brainstem Cerebellum" > ${csv_file}
+
+for i in $( ls ${output_dir}/* -d ); do
+
+	echo $( basename ${i} ) $( cat ${i}'/dice_score.txt' )
+	echo $( basename ${i} ) $( cat ${i}'/dice_score.txt' ) >> ${csv_file}
+
+done

run_test.sh

@@ -2,5 +2,10 @@
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
 project_id='60a14ca503bcad0ad27cada9'
 outputdir=$1
+download_dir=./'DBB_test'
 bash ${SCRIPT_DIR}/download_testset.sh
-bash ${SCRIPT_DIR}/predict_testset.sh proj-${project_id} ${outputdir}
+mkdir -p ${outputdir}
+tag_list=( ACC PFM MCDs HD )
+for tag in ${tag_list[@]}; do
+	bash ${SCRIPT_DIR}/predict_testset.sh ${download_dir}'/'${tag}'/'proj-${project_id} ${outputdir}'/'${tag}
+done

run_test_local.sh

@@ -0,0 +1,11 @@
+#! /bin/bash
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/"	
+project_id='60a14ca503bcad0ad27cada9'
+outputdir=$1
+download_dir=./'DBB_test'
+bash ${SCRIPT_DIR}/download_testset.sh
+mkdir -p ${outputdir}
+tag_list=( ACC PFM MCDs HD )
+for tag in ${tag_list[@]}; do
+	bash ${SCRIPT_DIR}/predict_testset_local.sh ${download_dir}'/'${tag}'/'proj-${project_id} ${outputdir}'/'${tag}
+done