#!/bin/sh

#   run_first_all - wrapper script for "run_first" (which wraps "first" - the main FIRST fitting)
#
#   Brian Patenaude, Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2006-2009 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 4.0 (c) 2007, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
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#   University harmless from and against any and all claims, damages and
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#   commercially. Use for which any financial return is received shall be
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#   innovation@isis.ox.ac.uk quoting reference DE/1112.

Usage() {
    echo ""
    echo "Usage: `basename $0` [options] -i <input_image> -o <output_image>"
    echo ""
    echo "Optional arguments:"
    echo "  -m <method>      : method must be one of auto, fast, none or a (numerical) threshold value"
    echo "  -b               : input is already brain extracted"
    echo "  -s <name>        : run only on one specified structure (e.g. L_Hipp) or a comma separated list (no spaces)"
    echo "  -a <img2std.mat> : use affine matrix (do not re-run registration)"
    echo "  -3               : use 3-stage affine registration (only currently for hippocampus)"
    echo "  -d               : do not cleanup image output files (useful for debugging)"
    echo "  -v               : verbose output"
    echo "  -h               : display this help message"
    echo ""
    echo "e.g.:  `basename $0` -i im1 -o output_name "
    exit 1
}


#########################################################################################################


# deal with options
structs="L_Accu L_Amyg L_Caud L_Hipp L_Pall L_Puta L_Thal R_Accu R_Amyg R_Caud R_Hipp R_Pall R_Puta R_Thal BrStem";
BETdone=no;
verbose=no;
doReg=yes;
bmeth=auto;
cleanUp=yes;
threestage=no;

if [ $# -eq 0 ] ; then Usage; exit 0; fi
# also accept old syntax for now (without -b option): <input_image> <threshold> <output_image>
if [ $# -eq 3 ] ; then
  iname=$1;
  bmeth="$2";
  oname=$3;
else
    args=`getopt i:o:m:s:a:bd3vh $*`
    if [ $? != 0 ] ; then 
	Usage
    fi
    set -- $args
    for i
      do
      case "$i"
	  in
	  -b)
	      BETdone=yes; 
	      flirtopts="-b" ; 
	      shift;;
	  -3)
	      threestage="yes";
	      shift;;
	  -v)
	      verbose=yes; 
	      shift;;
	  -h)
	      Usage;
	      exit 0;;
	  -d)
	      cleanUp=no;
	      shift;;
	  -i)
	      iname="$2";
	      shift 2;;
	  -o)
	      oname="$2";
	      shift 2;;
	  -m)
	      bmeth="$2";
	      shift 2;;
	  -a)
	      doReg=no; 
	      affmat="$2";
	      if [ ! -f $affmat ] ; then
		  echo "Error: cannot find affine matrix $affmat"
		  exit 1
	      fi
	      shift 2;;
	  -s)
	      structs=`echo "$2" | sed 's/,/ /g'`;
	      shift 2;;
      esac
    done
fi

if [ `${FSLDIR}/bin/imtest $iname` = 0 ] ; then
    echo "Error: cannot find image $iname"
    exit 1
fi
iname=`${FSLDIR}/bin/remove_ext $iname`

if [ $bmeth = FAST ] ; then bmeth=fast; fi
if [ $bmeth = NONE ] ; then bmeth=none; fi
if [ $bmeth = AUTO ] ; then bmeth=auto; fi
if [ $bmeth != fast ] && [ $bmeth != auto ] && [ $bmeth != none ] ; then
    thresh=$bmeth;
    bmeth=thresh;
fi

oname=`$FSLDIR/bin/remove_ext $oname`;

if [ $verbose = yes ] ; then echo "STRUCTURES: $structs" ; fi

# now do the work

logdir=${oname}.logs
if [ ! -d $logdir ] ; then mkdir $logdir ; fi

FLIRTJOBHOLD="";
if [ $doReg = yes ] ; then
    if [ -w `dirname $iname` ] ; then
	matname=${iname}_to_std_sub;
    else
	matname=${oname}_in_to_std_sub;
    fi
    if [ $threestage = yes ] ; then
	flirtopts="$flirtopts -strucweight $FSLDIR/data/standard/MNI152_T1_1mm_Hipp_mask_dil8"
    fi
    if [ $verbose = yes ] ; then echo ${FSLDIR}/bin/first_flirt $iname ${matname} $flirtopts ; fi
    FLIRTID=`${FSLDIR}/bin/fsl_sub -l $logdir -T 15 ${FSLDIR}/bin/first_flirt $iname ${matname} $flirtopts`
    FLIRTJOBHOLD="-j $FLIRTID"
    affmat=${matname}.mat
fi
COM=${oname}.com
/bin/rm -f ${COM}*

imscorr=""
imsfirst=""

for s in $structs; do
    modelN=336
    bcorr=1;
    intref=0;
    S_FIRST_4=`awk 'BEGIN {print substr("'$s'",3,4)}'`
    case "${S_FIRST_4}" in 
	Accu)
	    nmodes=50
	    ;;
	Amyg)
	    nmodes=50;
	    intref=1;
	    ;;
	Caud)
	    nmodes=30;
	    intref=1;
	    ;;
	Hipp)
	    nmodes=30;
	    intref=1;
	    ;;
	Late)
	    nmodes=40;
	    intref=1;
	    ;;
	Pall)
	    nmodes=40;
	    bcorr=0;	   
	    ;;
	Puta)
	    nmodes=40;
	    bcorr=0;	
	    ;;
	Thal)
	    nmodes=40;
	    bcorr=0;	
	    ;;
	Stem)
	    nmodes=40;
	    ;;
	*)
	    echo "Structure $s unknown"
	    exit 1
	    
    esac
    
    if [ "X$affmat" = X ] ; then
	echo "Error: affine matrix not specified";
	exit 1
    fi
    #run_first , choose between normal and intref
    imfirst="${oname}-${s}_first"
    imsfirst="${imsfirst} ${imfirst}"
    if [ $intref = 0 ] ; then 
	if [ $bcorr -eq 1 ] ; then 
	    ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/run_first -i $iname -t ${affmat} -n $nmodes -o ${imfirst} -m ${FSLDIR}/data/first/models_${modelN}_bin/${s}_bin.bmv\c" >> $COM
	else
	    ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/run_first -i $iname -t ${affmat} -n $nmodes -o ${imfirst} -m ${FSLDIR}/data/first/models_${modelN}_bin/05mm/${s}_05mm.bmv\c" >> $COM
	fi
    else
	S_CUT=`awk 'BEGIN {print substr("'$s'",1,1)}'`
	${FSLDIR}/bin/fslecho "${FSLDIR}/bin/run_first -i $iname -t ${affmat} -n $nmodes -o ${imfirst} -m ${FSLDIR}/data/first/models_${modelN}_bin/intref_thal/${s}.bmv -intref ${FSLDIR}/data/first/models_336_bin/05mm/${S_CUT}_Thal_05mm.bmv\c" >> $COM
    fi
    
    imcorr="${oname}-${s}_corr"
    imscorr="${imscorr} ${imcorr}"
    ##boundary correction
    if [ $bmeth = auto ] ; then
	# default is to use none for Thal,Puta,Pall and fast for the rest
	btype=fast;
	if [ $bcorr -ne 1 ] ; then btype=none; fi
    else
	btype=$bmeth;
	if [ $bmeth = thresh ] ; then btype="thresh -t $thresh"; fi
    fi
   ${FSLDIR}/bin/fslecho "; ${FSLDIR}/bin/first_boundary_corr -s ${imfirst} -o ${imcorr} -i $iname -b $btype" >> $COM
done

if [ $verbose = yes ] ; then cat $COM ; fi
FIRSTID=`${FSLDIR}/bin/fsl_sub -l $logdir -T 60 -N first $FLIRTJOBHOLD -t $COM`

if [ $btype = thresh ] ; then 
    threshnop=`echo $thresh | sed 's/\.//g'`
    methname=th${threshnop} ;
else
    methname=$btype ;
fi

numstruct=`echo $structs | wc -w`;
if [ $numstruct -gt 1 ] ; then 
    ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/fslmerge -t ${oname}_all_${methname}_firstseg ${imscorr} ; ${FSLDIR}/bin/fslmerge -t ${oname}_all_${methname}_origsegs ${imsfirst} ; ${FSLDIR}/bin/first_mult_bcorr -i $iname -u ${oname}_all_${methname}_origsegs -c ${oname}_all_${methname}_firstseg -o ${oname}_all_${methname}_firstseg" > ${COM}2
    if [ $verbose = yes ] ; then cat ${COM}2 ; fi
    MERGEID=`$FSLDIR/bin/fsl_sub -l $logdir -T 15 -N first_post -j $FIRSTID -t ${COM}2`
    MERGEHOLD="-j $MERGEID"
    
    if [ $cleanUp = yes ] ; then
	echo "${FSLDIR}/bin/imrm ${oname}-*_first* ${oname}-*_corr*" > ${COM}3
	if [ $verbose = yes ] ; then cat ${COM}3 ; fi
	$FSLDIR/bin/fsl_sub -l $logdir -T 5 -N clean_up $MERGEHOLD -t ${COM}3 
    fi
fi
