#!/bin/bash


#information at: http://www.nitrc.org/projects/art
# really not too much information! also run executables with -h for a little more information
# exemple d'execució: 

#definim parametres:
sourceDir=$1
fixed=$2
moving=$3 
outputDir=$4
lesionsBasal=$5
lesions12M=$6

drammsDir="/home/yago/Desktop/ImatgeMedica/prova/dramms/bin/"

#./dramms/bin/dramms-warp ./Moving.nii -r 0 campDramms.nii deformed.nii #r=0 for nearest neigborg 1 would be trilinear
#./dramms/bin/dramms -S ./Fixa.nii -T ./Moving.nii -c 1 -m 2 -O outputDramms.nii -D campDramms.nii -J jacobiaDramms.nii

echo "********************************************************************************************************** " 
echo "* Test DRAMMS, parameters:"
echo "* Fixed Images: $fixed"
echo "* MOving Image: $moving"
echo "* Prefix directori s: $outputDir"
echo "********************************************************************************************************** " 

echo " " 
echo "                        **************************************************************************************************** " 
echo "                                 TESTING DRAMMS "		  
echo " executo:	"
echo "                        **************************************************************************************************** " 


#execute registration
$drammsDir/dramms -S $fixed -T $moving -c 1 -m 2 -O outputDRAMMS.nii -D dispDRAMMS.nii -J jacobianDRAMMS.nii > sDRAMMS$outputDir.txt

mkdir filesDRAMMS\_$outputDir

#compute moved ground truth
cp $lesionsBasal ./lesionsBasal.nii
cp $lesions12M ./lesions12M.nii

$drammsDir/DRAMMS/dramms-warp lesions12M.nii -n dispDRAMMS.nii deformedLesions.nii #-n for nearest neigborg default would be trilinear

# compute difference images
$sourceDir/imageDifference $fixed outputDRAMMS.nii diffDRAMMS"After".nii
$sourceDir/imageDifference $fixed $moving diffDRAMMS"Before"$outputDir.nii

mv "diff"*.nii filesDRAMMS\_$outputDir
mv outputDRAMMS.nii filesDRAMMS\_$outputDir

#move lesion information
if ( "$temporalRegister" -eq true ) ; then
mv lesionsBasal.nii filesART\_$outputDir
mv lesions12M.nii filesART\_$outputDir
mv deformedLesions.nii filesART\_$outputDir 
fi

#move the rest
mv sDRAMMS$outputDir.txt filesDRAMMS\_$outputDir
mv dispDRAMMS.nii filesDRAMMS\_$outputDir
mv jacobianDRAMMS.nii filesDRAMMS\_$outputDir

