phantom-build

#!/bin/bash
####################################################################
#Configuration Set:
#--> Phantom simulation parameters
n=3                    #Noise level [0,3,9]		           (default: 0)
rf=20			             #RF field distortion [0,20,40] 	 (default: 0)
GM_VALUE=80		         #Gray Matter (ms) 		             (default: 80)
WM_VALUE=112		       #White Matter (ms) 		           (default: 112)
CSF_VALUE=200		       #CSF (ms) 			                   (default: 200)
R_TYPE=T2		           #Type of relaxometry [T1,T2] 	   (default: T2)
NUMBER_ECHOES=12 	     #Number of echos 		             (default: 12)
TE=0.012 		           #Time of echo (seconds) 	         (default: 0.012)
#
#--> If you want to change some parameters, please do this wisely
####################################################################

#n=${1:-$def_n}

# Check the softwares dependency
source scripts/dependency_check

OUTPUT_FOLDER=$1
#Check if the output folder selected exist
if [[ ! "`echo $OUTPUT_FOLDER`" == "" ]]; then
  if [[ ! -e $OUTPUT_FOLDER ]]; then
    echo "ERROR: The path for the output data do not exist!"
    echo "  Is it correct? $OUTPUT_FOLDER"
    exit
  fi
fi

if [[ "`echo $OUTPUT_FOLDER`" == "" ]]; then
  echo "-- Starting phantom reconstruction --"
  echo "#############################################"
  echo "Configuration set:"
  echo "Noise level                            = ${n}"
  echo "RF field distortion                    = ${rf}"
  echo "Gray Matter ${R_TYPE}                         = ${GM_VALUE}"
  echo "White Matter ${R_TYPE}                        = ${WM_VALUE}"
  echo "CSF Matter ${R_TYPE}                          = ${CSF_VALUE}"
  echo "Number of echos                        = ${NUMBER_ECHOES}"
  echo "Time of echo                           = ${TE}"
  echo "Output folder                          = relaxophantom/relaxo/"
  echo "#############################################"

  echo "Step 1: Volumes segmentation"
  ./scripts/phantom_segmentation $n $rf $R_TYPE
  echo "*** Step 1: Done ***"

  echo "Step 2: Phantom reconstruction"
  ./scripts/phantom_recon $n $rf $GM_VALUE $WM_VALUE $CSF_VALUE $R_TYPE $NUMBER_ECHOES $TE
  echo "*** Step 2: Done ***"

  echo "Step 3: Reformating relaxometry volumes"
  ./scripts/phantom_reformat ${n} ${rf} ${NUMBER_ECHOES} ${R_TYPE} ${TE}
  echo "*** Step 3: Done ***"

  # Removing empty relaxometry image Volumes
  for (( vol=153; vol<=180; vol++)); do
    rm `ls ${PWD}/relaxo/*0${vol}*`
  done

  echo "The results are located in the folder ./relaxo"
else
  echo "-- Starting phantom reconstruction --"
  echo "#############################################"
  echo "Configuration set:"
  echo "Noise level                            = ${n}"
  echo "RF field distortion                    = ${rf}"
  echo "Gray Matter ${R_TYPE}                         = ${GM_VALUE}"
  echo "White Matter ${R_TYPE}                        = ${WM_VALUE}"
  echo "CSF Matter ${R_TYPE}                          = ${CSF_VALUE}"
  echo "Number of echos                        = ${NUMBER_ECHOES}"
  echo "Time of echo                           = ${TE}"
  echo "Output folder                          = $OUTPUT_FOLDER"
  echo "#############################################"

  echo "Step 1: Volumes segmentation"
  ./scripts/phantom_segmentation $n $rf $R_TYPE
  echo "*** Step 1: Done ***"

  echo "Step 2: Phantom reconstruction"
  ./scripts/phantom_recon $n $rf $GM_VALUE $WM_VALUE $CSF_VALUE $R_TYPE $NUMBER_ECHOES $TE
  echo "*** Step 2: Done ***"

  echo "Step 3: Reformating relaxometry volumes"
  ./scripts/phantom_reformat ${n} ${rf} ${NUMBER_ECHOES} ${R_TYPE} ${TE}
  echo "*** Step 3: Done ***"

  #Changing output folder
  mv relaxo/ $OUTPUT_FOLDER

  # Removing empty relaxometry image Volumes
  for (( vol=153; vol<=180; vol++)); do
    rm `ls $OUTPUT_FOLDER/relaxo/*0${vol}*`
  done
  echo "The results are located in the folder $OUTPUT_FOLDER"
fi