organize_EvaluationSegmentation

#!/bin/bash
# Script to organize the output XML data from the quantitative segmentation metrics.

usage(){
  echo "  Script to organize the output XML data from the quantitative segmentation metrics."
  echo "    Usage: $(basename $0) <List of files> [Output name file]"
  echo ""
  echo "    <List of files> = A single file that lists all the segmentation evaluations from the output of EvaluateSegmentation toolkit. The segmentation metrics can be chosen arbitrarily and the full path to each file must be informed."
  echo "    [Output name file] = OPTIONAL: This is the output file name that will be saved the segmentation results. A CSV file should be useful. This file will be saved in the same directory of the listFilesList.txt file."
  echo ""
}
if [[ $# -lt 1 ]]; then
  usage
  exit
fi

LISTFILES=$1
OUTPUTNAME=$2

# Reorganize the metric output tables
echo " => Organizing segmentation evaluation..."
if [[ $OUTPUTNAME == "" ]]; then
  OUTPUTNAME=SegmentationOutput.csv
fi
printf "mask,DICE,JACRD,AUC,KAPPA,RNDIND,ADJRIND,ICCORR,VOLSMTY,MUTINF,MAHLNBS,AVGDIST,HDRFDST,VARINFO,GCOERR,PROBDST,SNSVTY,SPCFTY,PRCISON,FMEASR,ACURCY,FALLOUT,TP,FP,TN,FN,REFVOL,SEGVOL" >> $(dirname ${LISTFILES})/$OUTPUTNAME
printf "\n" >> $(dirname ${LISTFILES})/$OUTPUTNAME

for file in `cat ${LISTFILES}`; do
  echo "Organizing output file: $file"
  # File name
  printf "$(basename ${file})" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #DICE
  printf "`cat $file | grep DICE | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #JACRD
  printf "`cat $file | grep JACRD | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #AUC
  printf "`cat $file | grep AUC | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #KAPPA
  printf "`cat $file | grep KAPPA | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #RNDIND
  printf "`cat $file | grep RNDIND | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #ADJRIND
  printf "`cat $file | grep ADJRIND | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #ICCORR
  printf "`cat $file | grep ICCORR | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #VOLSMTY
  printf "`cat $file | grep VOLSMTY | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #MUTINF
  printf "`cat $file | grep MUTINF | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #MAHLNBS
  printf "`cat $file | grep MAHLNBS | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #AVGDIST
  printf "`cat $file | grep AVGDIST | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #HDRFDST
  printf "`cat $file| grep HDRFDST | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #VARINFO
  printf "`cat $file | grep VARINFO | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #GCOERR
  printf "`cat $file | grep GCOERR | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #PROBDST
  printf "`cat $file | grep PROBDST | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #SNSVTY
  printf "`cat $file | grep SNSVTY | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #SPCFTY
  printf "`cat $file | grep SPCFTY | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #PRCISON
  printf "`cat $file | grep PRCISON | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #FMEASR
  printf "`cat $file | grep FMEASR | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #ACURCY
  printf "`cat $file | grep ACURCY | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  #FALLOUT
  printf "`cat $file | grep FALLOUT | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # TP
  printf "`cat $file| grep TP | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # FP
  printf "`cat $file| grep FP | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # TN
  printf "`cat $file| grep TN | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # FN
  printf "`cat $file| grep FN | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # REFVOL
  printf "`cat $file| grep REFVOL | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  # SEGVOL
  printf "`cat $file| grep SEGVOL | awk '{print $3}'`" >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "," >> $(dirname ${LISTFILES})/$OUTPUTNAME
  printf "\n" >> $(dirname ${LISTFILES})/$OUTPUTNAME
done