renameSLEICSerDirs

#!/bin/bash

if [ "$#" -eq 0 ]; then
    TARGET=$( pwd )
else
    TARGET="$1"   
fi

[ ! -r "$TARGET" ] && echo "Target directory: $TARGET does not exist." && exit 1
cd $TARGET

#which dicom_hdr >/dev/null 2>&1
if command -v module >/dev/null && uname -a | grep -q aci.ics.psu.edu && ! command -v dicom_hdr >/dev/null; then
    module load afni 2>&1 >/dev/null
fi

serList=$( find . -regex ".*ser[0-9]+.*" -type d | sort -n | xargs -n 1 basename )
#serList=$( ls -d ser[0-9]* )
for s in ${serList}; do

    firstDicom=$( find "$s" -iname "1.3.12*" -type f -print -quit )
    
    if [ -z "${firstDicom}" ]; then
	echo "Unable to find any files of pattern 1.3.12* in dir: $s"
	exit 1
    fi

    sername=$( dicom_hdr $firstDicom | grep -i "ACQ Protocol Name" | perl -pe "s:.*ACQ Protocol Name//(\w+).*$:\1:" )
    sernumber=$( printf '%02d' ${s/ser/} )

    #is this a single-band reference image?    
    sbref=
    dicom_hdr $firstDicom | grep -q "REL Image Comments//Single-band reference" >/dev/null
    if [ $? -eq 0 ]; then
	sbref=_sbref
    fi

    mv "$s" "${sernumber}_${sername}${sbref}"
    echo "$s" > "${sernumber}_${sername}${sbref}/.origdirname"
    
done