dicomsort.sh

#!/bin/bash
#############
#This script use the afni programs dicom_hdr and dicom_hinfo to read header information, 
#reads the information and then renames and sorts the files alphabetically, optionally
#creating subdirectories for each series.  AFNI must be installed locally for 
#this script to work
#Written by Michael Worden
#Updated 02/07/2024 to add support for optionally creating subject and series 
#subdirectories
#Updated 03/15/2024 to name subdirectories by Series Description instead of Protocol Name
#############

set -euo pipefail

#defaults
sourcedir='./'
destdir='renamed'
tempfile='/tmp/dicomsort.tmp'
rename=0
recurse=1
usesubdir=0
subdir=''
useseqdir=0
seqdir=''

#DICOM field tags
snumtag='0020,0011'     #series number
anumtag='0020,0012'     #acquisition number
inumtag='0020,0013'     #instance number
nametag='0010,0010'     #patient name
idtag='0010,0020'       #patient ID
sdesctag='0008,103e'    #protocol name

usage='Usage: dicomsort [-r] [-d destdir] [-s sourcedir] [-i] [-q] [-n] [-h]'
helptxt="dicom sort is a script to sort rename dicom files in alphabetical order according to\n\
series and slice number.  AFNI must be installed on the local computer to use dicomsort."

#process command line options
while getopts ":rd:s:iqnh" options; do
  case $options in
    r ) rename=1;;
    d ) destdir=$OPTARG;;
    s ) sourcedir=$OPTARG;;
    i ) usesubdir=1;;
    q ) useseqdir=1;;
    n ) recurse=0;;
    h ) echo "$usage";;
    \? ) echo "$usage"
         echo -e "$helptxt"
#     	 echo "dicom sort is a script to sort rename dicom files in alphabetical"
#     	 echo "order according to series and slice number.  "
    	 echo "Options:"
    	 echo "-r: rename files.  Default is to copy."
    	 echo "-d: destination directoroy.  Default is ./renamed ."
    	 echo "-s: source directory.  Default is current directory"
    	 echo "-i: put files in a directory named by the subjectID."
    	 echo "-q: put files in separate sub-directories for each sequence."
    	 echo "-n: don't recursively descend into subdirectories."
    	 echo "-?: print this help message."
    	 echo "-h: print brief usage message."
         exit 1;;
    * ) echo "$usage"
          exit 1;;
  esac
done

#check to see if the destdir exists and create it if not
if [ -d "$destdir" ]; then
	echo Destination directory exists
else
	echo Creating "$destdir"
	mkdir "$destdir"	
fi
targdir="$destdir"

echo "Procecessing..."

#build a list of all the non-hidden files in the target directory
if [ "$recurse" -eq 1 ]; then
	files=$(find "$sourcedir" -type f ! -name ".*" ! -iname "DICOMDIR")
else
	files=$(find "$sourcedir" -type f -maxdepth 1 ! -name ".*" ! -iname "DICOMDIR")
fi	
	
for f in $files;
do
	echo "$f"
	
	#We are only using dicom_hdr to recognize dicom files now.  This seems clunky
	#and could probably be sped up in the future.  All valid dicom files should have 
	#the text DICM at offset 0x80 and we could just look for that in the future but 
	#this is okay for now
	dicom_hdr "$f" > "$tempfile" 
	
	# make sure it's a dicom file
	if grep 'ERROR:' "$tempfile"; then 
	  continue
	fi
	
	# Now using dicom_hinfo to get specific tags instead of dicom_hdr and grep
    snum=$(dicom_hinfo -tag "$snumtag" -no_name "$f")
    anum=$(dicom_hinfo -tag "$anumtag" -no_name "$f")
    if [ "$anum" = "null" ]; then    
        anum=0
    fi 
    inum=$(dicom_hinfo -tag "$inumtag" -no_name "$f")
	
	
	#If we want to use the the subject ID as an enclosing directory, check to see if
	#it exists and create it if not
	if [ "$usesubdir" -eq 1 ]; then
	    subdir=$(dicom_hinfo -tag "$nametag" -no_name "$f")
	    targdir="$destdir"/"$subdir"
		mkdir -p "${targdir}"
	fi
		
	#If we want to use subdirectories for each series, check to see if
	#it exists for the current series and create it if not.  The series name
	#should be prepended with a series number in case there are multiple 
	#series with the same sequence name.
	if [ "$useseqdir" -eq 1 ]; then
	    seqdir=$(dicom_hinfo -tag "$sdesctag" -no_name "$f")
	    serpre=$(printf "%02.0f_" "$snum")
	    targdir="$destdir"/"$subdir"/"$serpre$seqdir"
		mkdir -p "${targdir}"
	fi
	
	targfile=$(printf "%s/dcmS%04.0fA%04.0fI%04.0f\n" "$targdir" "$snum" "$anum" "$inum")
	
	echo "Series ${snum},  Acquisition ${anum},  Instance ${inum}"
	
	if [ "$rename" -eq 1 ]; then
		echo RENAMING "$f" to "$targfile"
		mv "$f" "$targfile"
	else
		echo COPYING "$f" to "$targfile"
		cp "$f" "$targfile"
	fi
	
done
rm "$tempfile"
echo dicomsort Complete