DICOM remap import script

#!/bin/bash

# Presumes the following environment variables are set:
#
# $SERVER
# $PROJECT
# $AETITLE
# $AEPORT
#
# This also presumes that:
#
# * Every folder name within the current directory maps to a subject ID
# * Every folder within the current directory contains only other folders or DICOM files
# * Each imported session should be named $SUBJECT_MR1
#
# Any function beyond that will require customization, but this does demonstrate walking
# a folder structure, finding all DICOM, anonymizing the data on the fly, and pushing the
# DICOM data to the XNAT server.

function createIfDoesntExist {
    URL=$1
    RESPONSE=$(curl --write-out %{http_code} --silent --output /dev/null -X GET -u admin:admin $URL)
    if [ "$RESPONSE" -eq "404" ]; then
        echo Creating object for $URL
        RESPONSE=$(curl --write-out %{http_code} --silent --output /dev/null -X PUT -u admin:admin $URL)
        if [ "$RESPONSE" != "200" -a "$RESPONSE" != "201" ]; then
            echo Something went wrong creating $URL, bailing out.
            exit
        fi
    fi
}

for SUBJECT in $(find . -mindepth 1 -maxdepth 1 -type d -printf "%P ")
do

    createIfDoesntExist http://${SERVER}/data/projects/$PROJECT/subjects/$SUBJECT

    echo Working directory $SUBJECT
    echo -e \(0008,1030\) := \""${PROJECT}"\" > script.das
    echo \(0010,0010\) := \""${SUBJECT}"\" >> script.das
    echo \(0010,0020\) := \""${SUBJECT}_MR1"\" >> script.das

    IMPORT=$(find $SUBJECT -mindepth 1 -maxdepth 1 -type d -printf "$SUBJECT/%P/ " | sed 's# #* #g')

    DicomRemap -d script.das -o dicom://$AETITLE@${SERVER}:$AEPORT/$AETITLE "$IMPORT"

done

# Clean up
[ -e script.das ] && { rm script.das; }