Uploads dicom images for a particular subject session to the tng xnat instance

uploaddcmtk.sh

#!/bin/bash
# uploads dicom images for a particular subject session to the tng xnat instance
# takes five arguments:
# 1: username - xnat username
# 2: password - xnat password
# 3: project - xnat project id
# 4: directory - the subdirectory that contains the session scan sud-directories
# 5: subject_id - the subject id associated with the session scan
#
# Assumptions!
# 1. There is a set of sub-directories under the specified directory each
# corresponding to a separate scan and that the dicom image files are all in
# those scan sub-directories.
# 2. The script is located in the same directory as the session directory

url="https://tng.psych.ox.ac.uk/xnat/data/archive/projects/$3"

# check for correct number of arguments
if [ "$#" -ne 5 ]; then
  echo -e "Incorrect number of arguments - expected 5"
  echo "Usage: uploaddcmtk.sh user password project directory subject"
else
  # check directory is an existing directory
  if [ -d $4 ]; then
    total_size=$(du -sh $4 | awk '{print$1}')
    cd $4
    # check for project
    project_exists=$(curl -silent -I -u $1:$2 $url)
    if [[ $project_exists == HTTP/1.1\ 200* ]]; then
      subject_id=$5
      # check for subject and create if it doesnt exist
      subject_exists=$(curl -silent -I -u $1:$2 $url/subjects/$subject_id)
      if [[ $subject_exists == HTTP/1.1\ 200* ]]; then
        echo "Using existing subject: $subject_id"
      else
        echo -n "Creating subject: $subject_id ("
        curl -X PUT -u $1:$2 $url/subjects/$subject_id
        echo " - created)"
      fi

      # check for existing session and bail if found
      session_exists=$(curl -silent -I -u $1:$2 $url/subjects/$subject_id/experiments/$4)
      if [[ $session_exists == HTTP/1.1\ 200* ]]; then
        echo "Found existing session: $4 - no files will be uploaded"
      else
        # create temp directory for dicoms which will be minorly altered before sending
        mkdir ../$4_temp

        # show progress bar
        total_dirs=$(find ./* -maxdepth 0 -type d | wc -l)
        echo -ne 'Sending dcm files: ['
        for i in $(seq 1 $total_dirs); do echo -n ' '; done;
        echo -ne ']\r'
        ((total_dirs--))
        num_dirs=0

        start_time="$(date +%s)"
        # iterate through scan sub-directories
        for d in */ ; do
          scan_size=$(du -sh $d | awk '{print$1}')
          scan_start_time="$(date +%s)"
          ((num_dirs++))
          # copy local dcm files
          cp $d* ../$4_temp/.
          # add patient comments dcm header field to indicate project, subject and session
          dcmodify -i "(0010,4000)=Project: $3; Subject: $subject_id; Session: $4" ../$4_temp/*
          # push dicom files to xnat
          storescu -aec XNAT tng.psych.ox.ac.uk 8104 ../$4_temp/*
          # remove local dcm files
          rm ../$4_temp/*
          # update progress bar
          scan_finish_time="$(date +%s)"
          scan_total_time=$((scan_finish_time-scan_start_time))
          echo "$4/$d - Sent $scan_size in $scan_total_time seconds"
          echo -n 'Sending dcm files: ['
          for i in $(seq 1 $num_dirs); do echo -n '#'; done
          for i in $(seq $num_dirs $total_dirs); do echo -n ' '; done
          echo -ne ']\r'
        done
        # remove temp directory
        rmdir ../$4_temp
        # conclude progress
        finish_time="$(date +%s)"
        total_time=$((finish_time-start_time))
        echo "$4 - Sent $total_size in $total_time seconds - Finished $(date)"
      fi
    else
      echo "project $3 not found - do the passed credentials have access to it?"
    fi
    cd ..
  else
    echo "unable to find directory $4"
  fi
fi