#!/bin/sh
# filename: viewercd.sh
#
# UTIL script: 22-Jun-2005 (eNlf v0.17)
#
# purpose    : rename & stack files
#
# notes      : specific for Philips Gemini PET/CT system
#

#
# vars
#
PATH=/usr/bin:/usr/sbin:/usr/ucb/bin:/usr/local/bin:/opt/sfw/bin
export PATH
DCMDICTPATH=/usr/local/dcmtk/lib/dicom.dic
export DCMDICTPATH
dcmdump=/usr/local/dcmtk/bin/dcmdump
spooldir="/home/patient/.viewercd"
dicomdir="$spooldir/dicom"
volumesdir="$spooldir/volumes"
lockfile="$spooldir/.lock"
wait=90 # number of 10 sec steps = 15 minutes
burndicom=no # burn dicom files on CD: yes|no
#
# functions
#
clean_up()
{
	/bin/rm -rf "$dicomdir"
	/bin/rm -rf "$volumesdir"
	/bin/rm -rf $spooldir/PETCT_*
	/bin/rm -f "$lockfile"
}

#
# init
#

ulimit -n 600

#
# go into spooldir
cd "$spooldir"

#
# only one process
if [ -r "$lockfile" ]; then

	exit 0
fi

#
# we`re running
touch "$lockfile"

#
# insert blank media
message -W 35 -D information -A "Insert blank media AFTER all image transfers are DONE. Waiting now for media to burn ViewerCD ..." &

#
# wait for blank media (max 15 minutes)
count=0
while [ ! -n "`/opt/sfw/bin/sudo cdrw -M 2>&1 | grep 'Media is blank'`" ] && [ $count -lt $wait ]
do
	sleep 10
	count=`expr $count + 1`
done;

if [ "$count" -eq $wait ]; then
	clean_up
	message -W 35 -D error "No blank media detected. Burning ViewerCD cancelled." &
	exit 1
fi
#
# sorted dicom spool
mkdir "$dicomdir"

#
# volumes dir
mkdir "$volumesdir"

#
# get all study subdirs
subdirs=`ls -d PETCT_*`
if [ -z "$subdirs" ]; then
	/bin/rm -f "$lockfile"
	message -W 35 -D error "No spooled files found. Burning ViewerCD cancelled." &
	exit 0
fi

#
# give sign of life
message -W 35 -D information -A "Processing ViewerCD files ..." &

#
# rename files & move from subdir + get distinct series
ctprev=""
ctseries=""
ptprev=""
ptseries=""
for subdir in $subdirs
do
	#
	# go into subdir
	cd "$subdir"

	#
	# CT files
	ctfiles=`ls CT*`
	if [ -n "$ctfiles" ]; then
		for ctfile in $ctfiles
		do
			#
			# get tags SeriesNumber 20,11 and InstanceNumber 20,13
			ctnmbrs=`$dcmdump --load-short --search "0020,0011" --search "0020,0013" --search-first $ctfile | sed 's/.*\[\(.*\)\].*/\1/g' | tr '\012' ' '`
			#
			# get slice number (= 1ST entry)
			ctslice=`echo $ctnmbrs | awk '{ printf("%05d\n",$1) }'`
			#
			# get distinct serie (= 2ND entry)
			ctserie=`echo $ctnmbrs | awk '{ printf("%05d\n",$2) }'`
			if [ "x$ctprev" != "x$ctserie" ]; then
				ctprev=$ctserie
				ctseries="$ctseries $ctserie"
			fi
			#
			# rename and move
			/bin/mv -f "$ctfile" "$dicomdir/CT$ctserie$ctslice.dcm"
			#echo $ctfile $ctserie $ctslice
		done
	fi

	#
	# PT files
	#
	ptfiles=`ls PI*`
	if [ -n "$ptfiles" ]; then
		for ptfile in $ptfiles
		do
			#
			# get MediaStorageSOPClassUID 0002,003
			ptuid=`$dcmdump --load-short --search-first --search "0002,0003" $ptfile | sed 's/.*\[\(.*\)\].*/\1/g'` 
			#
                        # get slicenr from filename
                        ptslice=`echo $ptuid | awk -F. '{ printf("%05d\n",$11) }'`
			#
                        # get distinct series
                        ptserie=`echo $ptuid | awk -F. '{ printf("%05d\n",$10) }'`
                        if [ "x$ptprev" != "x$ptserie" ]; then
                                ptprev=$ptserie
                                ptseries="$ptseries $ptserie"
                        fi
			# rename and move
			/bin/mv -f "$ptfile" "$dicomdir/PT$ptserie$ptslice.dcm"
			#echo $ptfile $ptserie $ptslice
		done
	fi

	#
	# go into spooldir
	cd "$spooldir"
	#
	# clean up subdir
	/bin/rm -rf "$subdir"
done

#
# stack files
#

#
# go into volumesdir
cd "$volumesdir"

#
# CT
for ctserie in $ctseries
do
	#
	# get first file
	firstfile=`/bin/ls -1 $dicomdir/CT$ctserie*.dcm | head -1`

	#
	# get ContrastBolusAgent
	ctcontrast=`$dcmdump --load-short --search "0018,10" --search-first $firstfile | sed 's/.*\[\(.*\)\].*/\1/g' | awk '{ print $1 }'`

	#
	# get PatientPosition
	ctpatposition=`$dcmdump --load-short --search "0018,5100" --search-first $firstfile | sed 's/.*\[\(.*\)\].*/\1/g' | awk '{ print $1 }'`

	#
	# get all slices, properly sorted
	if [ "x$ctpatposition" = "xHFS" ]; then
		# HFS = reverse slice order
		allslices=`/bin/ls $dicomdir/CT$ctserie*.dcm | sort -rn`
        else
		# FFS = keep slice order
		allslices=`/bin/ls $dicomdir/CT$ctserie*.dcm | sort -n`
        fi

	#
	# stack CT
	medcon -s -one -f $allslices -c intf -o UZG-CT-$ctserie-$ctcontrast -stack3d -noprefix
done

#
# PT
for ptserie in $ptseries
do

	#
	# get first file
	firstfile=`/bin/ls $dicomdir/PT$ptserie*.dcm | head -1`

	#
	# get type of attenuation correction: NAC, AC, CTAC, CTAC_B
	#ptattn=`strings $firstfile | grep "Attenuation Cor" | sed 's/Attenuation Cor=\(.*\),.*/\1/g'`
	ptattn=`$dcmdump --load-short --search "7053,1003" --search-first $firstfile | sed 's/.*\[p[0-9]*s[0-9]*_.*_\(.*\)\.img\].*/\1/g' | /usr/xpg4/bin/tr '[:lower:]' '[:upper:]'`

	#
	# get all slices, properly sorted
	allslices=`/bin/ls $dicomdir/PT$ptserie*.dcm | sort -n`

	#
	# stack PT
	medcon -qc -b16 -s -one -f $allslices -c intf -o UZG-PT-$ptserie-$ptattn -stack3d -noprefix
done

#
# go into spooldir
cd "$spooldir"

#
# burn dicom on CD?
if [ "x$burndicom" = "xno" ]; then
	/bin/rm -rf "$dicomdir"
fi

#
# burn cd
/usr/local/bin/make-cdrom -c -g "$spooldir"

#
# clean up
clean_up

#
# leave
exit 0