dicom_dirSend.bash

#!/bin/bash

# "include" the set of common script functions
source common.bash

declare -i Gb_customStorescu=0
declare -i Gi_verbose=0
declare -i Gb_anonymize=0
declare -i Gb_partialAnonymize=0
declare -i Gb_keepAnonymize=0
declare -i Gb_overrideMRN=0

G_STORESCU="storescu"
G_FILEEXT=""
G_HOST=fnndsc.tch.harvard.edu
G_AETITLE="DCM4CHEE"
G_CAETITLE="CDCM4CHEE"
G_LISTENPORT=11112
G_SSLCERTIFICATE="/neuro/users/chris/anonymize_key/CA_cert.pem"
G_ANONOUTDIR=""
G_SUBJECTNAME="anonymized"
G_MRN="anonymized"

G_SYNOPSIS="


 NAME

	dicom_dirSend.bash

 SYNOPSIS

        dicom_dirSend.bash	[-v <verbosity>]                	\\
                                [-a <aetitle>]				\\
                                [-h <dicomHost>]			\\
                                [-p <listenPort>]			\\
                                [-s <storescu>]				\\
                                [-A]                        		\\
                                [-P] [-N <SubjName>] [-M <MRN>]         \\
                                [-k]                        		\\
                                [-K <SSLCertificate>        		\\
                                [-O <anonOutputDir>]              	\\
                                [-E <fileExt>]              		\\
				<dicomDir1> <dicomDir2> ... <dicomDirN>

 DESCRIPTION

        'dicom_dirSend' is a shell wrapper that recursively sends a 
	group of directories containing DICOM images to a remote
	PACS server.

 PRECONDITIONS

	o common.bash script source.

 ARGUMENTS

        -v <level> (Optional)
        Verbosity level. A value of '10' is a good choice here.
        
        -A (Optional)
        If specified, anonymize data before transmission.
        
        -P (Optional)
        If specified, do a partial anonymization of the data (similar to -A,
        but rather than doing a full DICOM-compliant anonymize, only anonymizes
        some of the fields).

        -N <SubjName>
        In conjunction with -P, specifies the subject name field to inject
        into the anonymized DICOMS. Otherwise reverts to 'anonymous'.

        -M <MRN>
        In conjunction with -P, specifies the MRN field to inject into the
        anonymized DICOMS. Otherwise, anon MRN is a md5 hash of original MRN.

        -k (Optional)
        If specified, do not delete (keep) the anonymized directory 
                
        -E <fileExt> (Optional)
        If specified, only transmit files ending in *.<fileExt>, otherwise
        transmit all files in the target directory. Specifying the 
        <fileExt> is useful, since the transmission program will
        fail if attempting to transmit non-dicom files.

        -a <aetitle> (optional, default = $G_AETITLE)
        The aetitle of the PACS process to receive the data.
        
        -c <aetitle> (optional, default = $G_CAETITLE)
        The called aetitle of the PACS process to receive the data.

        -h <remoteNMRhost> (optional, default = $G_HOST)
        The host running the PACS process, i.e. the hostname of the DICOM
        peer.

        -p <listenPort> (optional, default = $G_LISTENPORT)
        The port number on which the PACS process is listening.

        -K <SSLCertificate> (optional, default = $G_SSLCERTIFICATE)
        The anonymization process ('gdcmanon') requires an SSL certificate.  
        If requesting anonymization, the process to generate an SSL certificate 
        is described at: http://gdcm.sourceforge.net/html/gdcmanon.html

        -O <anonOutDir> (optional, default = $G_ANONOUTDIR)
        The directory where the anonymized files will be stored

        -s <storescu> (optional, default = $G_STORESCU)
        Use this option to specify a <storescu> binary, typically used
        if <storescu> is not on the standard PATH. The basename of
        <storescu> is assumed to also contain any necessary libraries.

        <dicomDir1> <dicomDir2> ... <dicomDirN>
        The list of DICOM directories to transmit to the PACS process.

 EXAMPLES

  o To transmit to the dcmtk server on 'kaos':

    $>dicom_dirSend.bash -v 10 -a ELLENGRANT -h kaos.nmr.mgh.harvard.edu \\
      -p 10401 -E dcm <DIR1>... <DIRn>

  o To anonymize and override MRN and SubjectName:

    $>dicom_dirSend.bash -v 10 -a ELLENGRANT -h kaos.nmr.mgh.harvard.edu \\
      -p 10401 -P -M ANON-MRN -N ANON-NAME <DIR1>... <DIRn>

"

###\\\
# Globals are in capital letters. Immutable globals are prefixed by 'G'.
###///
G_SELF=`basename $0`
G_PID=$$

# Actions
A_fileCheck="checking on 'storescu'"
A_dirlistCheck="checking for the DICOM directory list"
A_dirCheck="checking the DICOM directory access"
A_storescu="executing the 'storescu' process"
A_dirAccess="attempting to access a directory"

# Error messages
EM_fileCheck="I couldn't find the 'storescu' executable on your path."
EM_dirlistCheck="no DICOM directory list was specified!"
EM_dirCheck="the DICOM directory could not be accessed."
EM_storescu="an error was returned."
EM_dirAccess="I couldn't access the directory. Does it exist? Do you have access rights?"

# Error codes
EC_fileCheck="10"
EC_dirlistCheck="20"
EC_dirCheck="30"
EC_storescu="40"
EC_dirAccess="50"

###\\\
# Function definitions
###///

###\\\
# Process command options
###///

while getopts v:a:c:h:p:s:APkE:K:O:N:M: option ; do
        case "$option"
        in
                v) Gi_verbose=$OPTARG			;;
                A) Gb_anonymize=1                       ;;
                P) Gb_partialAnonymize=1                ;;
                M) G_MRN=$OPTARG
                   Gb_overrideMRN=1                     ;;
                N) G_SUBJECTNAME=$OPTARG                ;;
                k) Gb_keepAnonymize=1                   ;;
                K) G_SSLCERTIFICATE=$OPTARG             ;;
                O) G_ANONOUTDIR=$OPTARG                 ;;
                E) G_FILEEXT=".${OPTARG}"               ;;
                a) G_AETITLE=$OPTARG                    ;;
                c) G_CAETITLE=$OPTARG                   ;;
                h) G_HOST=$OPTARG                       ;;
                p) G_LISTENPORT=$OPTARG                 ;;
                s) G_STORESCU=$OPTARG					
                   Gb_customStorescu=1                  ;;
                \?) synopsis_show
                    exit 0;;
        esac
done

topDir=$(pwd)
verbosity_check

REQUIREDFILES="$G_STORESCU"
for file in $REQUIREDFILES ; do
        statusPrint	"Checking for $file..."
        file_checkOnPath $file || fatal fileCheck
done

if (( Gb_customStorescu )) ; then
	DIRNAME=$(dirname $G_STORESCU)
	statusPrint	"Checking <storescu> dirname"
	cd $DIRNAME	>/dev/null
	ret_check $? || fatal dirAccess
	DIRNAME=$(pwd)
	export DCMDICTPATH=$(pwd)/dicom.dic
	cd $topDir	>/dev/null
fi

shift $(($OPTIND - 1))
declare -i b_DCMLIST=0
DCMLIST=$*
b_DCMLIST=$(echo $DCMLIST | wc -w)

if (( !b_DCMLIST )) ; then
	fatal dirlistCheck
fi

if (( ${#G_FILEEXT} )) ; then
    cprint "DICOM file extension"       "[ $G_FILEEXT ]"
fi

topDir=$(pwd)
for DIR in $DCMLIST ; do
	statusPrint	"Checking access to $DIR" "\n"
        lprint          "Access check"
	dirExist_check "$DIR" || fatal dirCheck
        if (( Gb_anonymize  || Gb_partialAnonymize)) ; then
            statusPrint "Anonymizing $DIR..." "\n"
            INPUTDIR=$DIR
            if [ -z "$G_ANONOUTDIR" ]; then
              OUTPUTDIR=${DIR}-anon
            else  
              OUTPUTDIR=$G_ANONOUTDIR
            fi
            ANONARG=""
            if ((Gb_partialAnonymize)) ; then
            	ANONARG=" -P -N $G_SUBJECTNAME "
                if (( Gb_overrideMRN )) ; then
                    ANONARG="$ANONARG -M $G_MRN "
                fi
            fi
            CMD="dcmanon_meta.bash -v 10 -K $G_SSLCERTIFICATE -D $INPUTDIR -O $OUTPUTDIR $ANONARG"
            echo "$CMD" | sh -v
            DIR=$OUTPUTDIR
            cprint      "Anonymization" "[ ok ]"
        fi
        statusPrint	"Transmitting *$G_FILEEXT files in $DIR..." "\n"
        cd "$DIR" >/dev/null
        CMD="$G_STORESCU -aet $G_AETITLE -aec $G_AETITLE $G_HOST $G_LISTENPORT *${G_FILEEXT}"
	cprint "Command: " "$CMD"
        lprint          "Transmission"
        eval "$CMD"
        ret_check $? || fatal storescu
        cd ../
        if (( !Gb_keepAnonymize && ( Gb_anonymize || Gb_partialAnonymize) )) ; then
            lprint      "Removing temp directory"
            rm -fr "$DIR"
            rprint      "[ ok ]"
        fi
done

shut_down 0