dcm_batch.bash

#!/bin/bash

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

declare -i Gi_verbose=0
declare -i Gb_useOverrideOut=0
declare -i Gb_forceStage=1
declare -i Gb_scanAll=0

DICOMDIR="/chb/users/dicom/files"
MRISLIST=""
G_SYNOPSIS="

 NAME

        dcm_MRIDget.bash

 SYNOPSIS

        dcm_MRIDget.bash        [-v <verbosity>]                \\
                                [-d <dicomDir>]                 \\
                                [-a]                            \\
                                [<DICOMDIR1> <DICOMDIR2> ... <DICOMDIRn>]

 DESCRIPTION

        'dcm_MRIDgetXML.bash' targets a given <dicomDir>, and for each
        subdirectory, checks for the MRID.

 ARGUMENTS

        -v <level> (optional)
        Verbosity level.

        -d <dicomDir> (optional)
        The 'root' directory containing dicom subdirs.
        Defaults to $DICOMDIR.

        -a (optional)
        Scan all directories in <dicomDir>. By default, the script will
        only flag the first directory containing the MRID. For multiple
        scans of the same MRID, the *entire* directory needs to be scanned.

        <DICOMDIR1> <DICOMDIR2> ... <DICOMDIRn>
        A list of target DICOM dirs. If specified, dcm_MRIDget will only search
        for these DICOM dirs, otherwise all MRIDs in <dicomDir> will be shown.

 PRECONDITIONS
        
        o Assumes that the <dicomDir> is a 'root' directory containing 
          subdirectories, each of which contains dicoms for a particular 
          MRID.
        o FreeSurfer env.

 POSTCONDITIONS

        o For each subdir in <dicomDir>, the MRID associated with each
          subdir is displayed. If a MRID is specified on the command line
          the script will only output the particular subdirectory containing
          the passed MRID.

 HISTORY

        12 March 2010
        o Initial design and coding.
"

###\\\
# Globals are in capital letters. Immutable globals are prefixed by 'G'.
###///

# Actions
A_noDCMFILE="checking for <DCMFILE>"
A_noDICOMDIR="checking on <dicomDir>"
A_noSubjectsDirVar="checking environment"

# Error messages
EM_noDCMFILE="could not read <DCMFILE>."
EM_noDICOMDIR="could not find <dicomDir>."
EM_noSubjectsDirVar="it seems that the SUBJECTS_DIR environment var is not set."

# Error codes
EC_noDCMFILE=1
EC_noDICOMDIR=2
EC_noSubjectsDir=10

# Defaults
D_whatever=

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


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

while getopts d:v:a option ; do 
        case "$option"
        in
                d) DICOMDIR=$OPTARG ;;
                a) let Gb_scanAll=1 ;;
                v) let Gi_verbose=$OPTARG ;;
                \?) synopsis_show 
                    exit 0;;
        esac
done

verbosity_check
topDir=$(pwd)

printf "%40s"   "Checking for SUBJECTS_DIR env variable"
b_subjectsDir=$(set | grep SUBJECTS_DIR | wc -l)
if (( !b_subjectsDir )) ; then
        fatal noSubjectsDirVar
fi
ret_check $?

printf "%40s"   "Checking for <dicomDir>"
dirExist_check $DICOMDIR || fatal noDICOMDIR
cd $DICOMDIR ; DICOMDIR=$(pwd) ; cd $topDir

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

cd $DICOMDIR
let hitCount=0
let b_hit=0
exec 1>&6 6>&-
if (( !b_DCMLIST )) ; then
    echo "<?xml version=\"1.0\"?>"
fi

for DIR in * ; do
    dirExist_check $DIR >/dev/null
    if (( !$? )) ; then 
        cd "$DIR" >/dev/null 2>/dev/null; 
        DCMMKINDX=""
        if [ -f toc.txt ] ; then    
	    dcm_mkIndx.bash -a > toc.txt
        fi

        cd $DICOMDIR; 
    fi
done

verbosity_check
if (( b_hit )) ; then
        shut_down 0
else
        shut_down 1
fi