preprocessDistortion

#!/usr/bin/env bash
set -eo pipefail

ppdistortion_usage() {
   cat  >&2 <<HEREDOC
USAGE:
  preprocessDistortion -phasedir path/to/fm_phase_dicoms/ -magdir path/to/fm_mag_dicoms/ -fm_cfg protocol_cfg [-mrpatt "MR*" ] [-savedir $(pwd) ] [-reverse]

  manditory:
    -phasedir and -magdir ||  -mag and -phase || -mag  -real -complex || -niidir
    -fm_cfg     info about protocols, mabye optional
  optional:
    -mrpatt     what dicoms look like
    -savedir    where to save outputs
    -reverse    NCANDA reverse (all but site C)
    -method     gre.nii.gz,gre,NCANDA,BIDSFM

HEREDOC
exit 1
}

# get all the things we need
sourceall() {
 local scriptdir=$(dirname $0)
 local sourcedir=$scriptdir/preproc_functions
 [ ! -d $sourcedir ] && echo "bad source dir! $sourcedir" >&2 && exit 1
 for f in convert_or_use_nii waitforlock prepare_gre_fieldmap \
          helper_functions preprare_fieldmap_ge_complex;do
   source $sourcedir/$f
 done
}

val2ARG(){ local s="$1"; s=${s:1}; s=${s^^}; echo "$s";}

set_method(){
  [ -n "$METHOD" ] && return 0
  local sep="xxxxxxxxx"
  local all_ge=$MAG$sep$COMPLEX$sep$REAL$sep
  # just mag is okay.  but complex or real without the other 2 is a problem
  [[ $all_ge =~ $sep$sep ]] && ! [[ $all_ge =~ ^$sep$sep$sep$ ]] &&
  exiterr "GE needs all -mag -complex and -real"

  ## set METHOD
  #  20191107: only gre (Siemens, Hallquist) and ge (NCANDA)
  #            BIDSFM works for siemens ncanda. might work for BIDS too
  [[ $all_ge =~ ^$sep$sep$sep$ ]]  && METHOD="gre" || METHOD="ge"

  # NIIDIR is setup to be NCANDA raw dir
  # but might be adapted for BIDS compatible directory
  if [[ -n "$NIIDIR" ]]; then
     # if we have a "real" nifti file it's ncanda
     [ -n "$(find "$NIIDIR" -maxdepth 1 -iname '*real*nii*'\
                 \( -type f -or -type l \) -print -quit)" ] &&
         METHOD="NCANDA" ||
         METHOD="BIDSFM" # TODO: does this work for actual bids spec?
  fi
}

say_globals(){
    # for debuging, print settings
    for var in  REVERSE NIIDIR PHASEDIR MAGDIR MAG PHASE\
        REAL COMPLEX FM_CFG MRPATT SAVEDIR METHOD; do
    [ -z "${!var}" ] && continue
    eval 'echo '"$var"': ${'"$var"'[@]}'
    done
 }
parsenewargs(){
    local setting=""
    local val=""
    [ $# -lt 1 ] && ppdistortion_usage;
    while [ -n "$1" ]; do
    case "$1" in
        -h|-help) ppdistortion_usage;;
        -r|-reverse) REVERSE="1"; shift ;;
        # 20201016 added mag back, add method
        -phasedir|-magdir|-mag|-phase|-fm_cfg|-mrpatt|-savedir|-niidir|-method)
        setting="$(val2ARG "$1")"
        val="$2"
            # remove default unless value could be an array arg
        ! [[ $setting =~ MAG|REAL|COMPLEX ]] && unset $setting; 
        shift 2;;
        -*) exiterr "unkown switch '$1'";;
        *)
        # if not -arg, add to the last -arg given
        [ -z "$setting" ] && exiterr "dont know what to set as '$1'";
        val="$1"
        shift
        ;;
    esac
    if [ -z "${!setting}" ]; then
        # everything is an array. if only one item e.g. $MAGDIR will get it
        # NB. -ag will not work in bash 4. need bash 5
        eval "declare -ag $setting=\"$val\"";
    else
        # not sure if there is another way to extend an array with varaible name
        # using mixed '' and "" like 'literal '"$intereted"' more litteral'
        eval "declare -ag $setting"'=(${'"$setting"'[@]}'" $val )"
    fi
    done
    # sanity check
    [ -n "$PHASEDIR" -a -n "$PHASE" ] && exiterr "give -phase or -phasedir, not both" 
    [ -n "$MAGDIR" -a -n "$MAG" ] && exiterr "give -mag or -magdir, not both" 
    [ -n "$NIIDIR" -a -n "$MAG" ] && exiterr "-niidir only if no other nifitis to provide" 
    [ -n "$PHASEDIR"  -o -n "$PHASE" ] && [ -n "$COMPLEX" -o -n "$REAL" ] &&
    exiterr "phase cannot be used with complex/real" 

    set_method
    
    say_globals
}


testExpected() {
   # return true if all expected files exist
   # global EXPECT,HAVEEXPECT, SAVEDIR
   HAVEEXPECT=()
   for f in "${EXPECT[@]}"; do
      [ -r "$SAVEDIR/$f" ] && HAVEEXPECT=(${HAVEEXPECT[@]} $f)
   done

   [ ${#HAVEEXPECT[@]} -eq ${#EXPECT[@]} ] 
}

_preprocessDistortion() {
   starttime=$(date +%s)
   # optional defaults
   SAVEDIR=$(pwd)
   MRPATT="MR*"
   REVERSE="0"
   # helperFunctions uses this for rel
   export logFile="preprocessDistortion.log"


   ## prepare
   # get functions and args
   sourceall 
   parsenewargs "$@"

   # needed for some functions
   export fm_cfg="$FM_CFG"

   ## did we already finish? 
   # EXPECT=( FM_UD_fmap_mag{,_brain}.nii.gz \
   #          unwarp/FM_UD_fmap{,_mag}.nii.gz \
   #          .fieldmap_{magnitude,phase} )
   EXPECT=( FM_UD_fmap_mag{,_brain}.nii.gz \
            unwarp/FM_UD_fmap{,_mag}.nii.gz )

   testExpected && echo "skipping '$SAVEDIR'; have all final files: ${HAVEEXPECT[@]}" && exit 0
   local theseargs="$@"
   rel "RUNNING: $0 $theseargs" c

   if [ ${#HAVEEXPECT[@]}  -gt 0 ] ; then
      rel "rm -r $SAVEDIR; # and try again; have ${#HAVEEXPECT[@]}/${#EXPECT[@]} expected files: ${HAVEEXPECT[@]}" c 
      exit 1
   fi

   [ -r "$SAVEDIR/phase" -o -r "$SAVEDIR/mag" ] && 
       rel "have $SAVEDIR/{phase,mag} but did not run prepare, remove $SAVEDIR and try again?" c && exit 1


   ## get files
   [ -z "$SAVEDIR" ] && echo "ERROR missing SAVEDIR!" && return 1
   [ ! -d $SAVEDIR ] && mkdir $SAVEDIR
   SAVEDIR="$(readlink -f "$SAVEDIR")"

   # functions create unwarp and cd into it
   case $METHOD in
      gre.nii.gz)
       cd $SAVEDIR
       prepare_gre_fieldmap "$MAG" "$PHASE"
      ;;

      gre)
       magdir="$MAGDIR"
       phasedir="$PHASEDIR"
       [ -z "$magdir" -o -z "$phasedir" ] && echo "ERROR: no magdir or phasedir!? $magdir $phasedir" && return 1
       rel "cp -r \"$magdir\" \"$SAVEDIR/mag\" "
       rel "cp -r \"$phasedir\" \"$SAVEDIR/phase\" "
       cd $SAVEDIR

       # run
       fm_phase="phase/$MRPATT"
       fm_magnitude="mag/$MRPATT"
       prepare_gre_fieldmap 
       ;;
      NCANDA)
       NIIDIR="$(readlink -f $NIIDIR)"
       cd $SAVEDIR
       prepare_fieldmap_ge_complex "$NIIDIR" $REVERSE
       ;;
      BIDSFM)
       NIIDIR="$(readlink -f $NIIDIR)"
       cd $SAVEDIR
       # TODO: look for json that has "intended for" instead of just using the first
       # take the first mag
       mag=$(find $NIIDIR -maxdepth 1 \( -type f -or -type l \) -iname '*mag*.nii.gz' -print -quit)
       # and first phase
       phase=$(find $NIIDIR -maxdepth 1 \( -type f -or -type l \) -iname '*phase*.nii.gz' -print -quit)
       [ -z "$mag" -o -z "$phase" ] && exiterr "cant find phase and mag nii.gz in $NIIDIR!"
       prepare_gre_fieldmap $mag $phase
       ;;
      *)
         exiterr "unknown unwarp method '$METHOD'";
    esac
    # all methods should drop into "unwarp"
    ! [[ $(basename $(pwd)) == unwarp ]] && exiterr "w/'$METHOD': in cwd '$(pwd)' is not 'unwarp' directory"

    # bet'ed brain needs to be in unwarp directory
    [ ! -r FM_UD_fmap_mag_brain.nii.gz -a -r ../FM_UD_fmap_mag_brain.nii.gz ] &&
      cp ../FM_UD_fmap_mag_brain.nii.gz ./
    [ ! -r FM_UD_fmap_mag_brain.nii.gz ] &&
      echo "WARNING: missing $(pwd)/FM_UD_fmap_mag_brain.nii.gz !"

   # also need the FM_UD from fm_phase -- actually have it already!
   #[ -r fm_phase/FM_UD_fmap.nii.gz -a -d unwarp ] && cp fm_phase/FM_UD_fmap.nii.gz unwarp/

   # copy config to save directory
   fmcfgfile=$(find_fmconfig $FM_CFG)
   [ -z "$fmcfgfile" -o ! -r "$fmcfgfile" ] && exiterr "cannot find config file '$FM_CFG', how did the above work!?"
   rel "cp $fmcfgfile $SAVEDIR/unwarp/fm.cfg"

   ! testExpected && echo "DID NOT FINISH '$SAVEDIR'; have ${HAVEEXPECT[@]}, want ${EXPECT[@]}" && exit 1

   # all done
   rel "$(date) Finished distortion preprocessing" c

   # write git version in completed file flag 
   command -v preprocessDistortion || return 0 # if sourcing, this doesn't makes sense
   gitver=$(cd $(dirname $(which preprocessDistortion )); git log --pretty=format:'%ci %h' -n 1)
   echo -e "$gitver\t$(date +%FT%H:%M)\t$(whoami)@$(hostname)\t$starttime\t$(date +%s)" > $SAVEDIR/.preprocessDistortion_complete
}

# if we did not source this file
# but ran it like ./preprocessDistortion
# actually run
[ $(basename $0 ) == "preprocessDistortion" ] && 
  _preprocessDistortion "$@"