#!/bin/sh

#   standard_space_roi - align input image to standard space and
#   output ROI version of input that matches the standard space FOV
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2005-2007 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
#   
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# {{{ Usage()

Usage() {
    cat <<EOF

Usage: standard_space_roi <input> <output> [options] [flirt options]

This masks the input and/or reduces its FOV, on the basis of a
standard space image or mask, that is transformed into the space
of the input image.

Masking options (applied before FOV-reduction):
  -maskFOV           : mask output using transformed standard space FOV (default)
  -maskMASK <mask>   : mask output using transformed standard space mask
  -maskNONE          : do not mask output

FOV-reduction options:
  -roiFOV            : cut down input FOV using bounding box of the transformed standard space FOV (default)
  -roiMASK <mask>    : cut down input FOV using nonbackground bounding box of the transformed standard space mask
  -roiNONE           : do not cut down input FOV

With either MASK option, <mask> must be in the same space as the standard space reference image.

Other options:
  -ssref <ref_image> : standard space reference image to use (default ${FSLDIR}/data/standard/MNI152_T1)
  -altinput <image>  : alternative input image to apply the ROI to (instead of the one used to register to the reference)
  -d                 : debug (don't delete intermediate files)
  -b                 : betpremask, equivalent to: -maskMASK ${FSLDIR}/data/standard/MNI152_T1_2mm_brain_mask_dil -roiNONE

All above options must come before any flirt options.

EOF
    exit 1
}

# }}}

# {{{ parse main arguments

[ _$2 = _ ] && Usage

in=`${FSLDIR}/bin/remove_ext $1`
if [ `${FSLDIR}/bin/imtest $in` = 0 ] ; then
    echo "Input image $in not valid"
    exit 1
fi
shift

out=`${FSLDIR}/bin/remove_ext $1`
shift

# }}}
# {{{ parse other options

debug=0
standard=${FSLDIR}/data/standard/MNI152_T1_2mm
inapply=$in
roi=1
mask=1

while [ _$1 != _ ] ; do

    if [ $1 = -d ] ; then
        debug=1
        shift
    elif [ $1 = -b ] ; then
        maskthr="-thr 0.5"
	mask=2
        maskmask=${FSLDIR}/data/standard/MNI152_T1_2mm_brain_mask_dil
	roi=3
        shift
    elif [ $1 = -ssref ] ; then
	[ _$2 = _ ] && Usage
	standard=$2
	shift 2
	if [ `${FSLDIR}/bin/imtest $standard` = 0 ] ; then
	    echo "standard space reference image not valid"
	    exit 1
	fi
    elif [ $1 = -altinput ] ; then
	[ _$2 = _ ] && Usage
	inapply=$2
	shift 2
	if [ `${FSLDIR}/bin/imtest $inapply` = 0 ] ; then
	    echo "Input image $inapply not valid"
	    exit 1
	fi

    elif [ $1 = -roiFOV ] ; then
        roi=1
        shift
    elif [ $1 = -roiMASK ] ; then
        roi=2
	[ _$2 = _ ] && Usage
	roimask=$2
	shift 2
	if [ `${FSLDIR}/bin/imtest $roimask` = 0 ] ; then
	    echo "Image $roimask not valid"
	    exit 1
	fi
    elif [ $1 = -roiNONE ] ; then
        roi=3
        shift

    elif [ $1 = -maskFOV ] ; then
        mask=1
        shift
    elif [ $1 = -maskMASK ] ; then
        mask=2
	[ _$2 = _ ] && Usage
	maskmask=$2
	shift 2
	if [ `${FSLDIR}/bin/imtest $maskmask` = 0 ] ; then
	    echo "Image $maskmask not valid"
	    exit 1
	fi
    elif [ $1 = -maskNONE ] ; then
        mask=3
        shift

    else
	break
    fi

done

# echo debug=$debug
# echo standard=$standard
# echo inapply=$inapply
# echo roi=$roi
# echo mask=$mask
# echo roimask=$roimask
# echo maskmask=$maskmask
# echo flirtopts=$@

# }}}
# {{{ do the work...

${FSLDIR}/bin/flirt -in $in -ref $standard -o ${out}_tmp_to_std -omat ${out}_tmp_to_std.mat $@
${FSLDIR}/bin/convert_xfm -inverse -omat ${out}_tmp_to_std_inv.mat ${out}_tmp_to_std.mat

X=`${FSLDIR}/bin/fslval $standard dim1` ; X=`echo "$X 2 - p" | dc -`
Y=`${FSLDIR}/bin/fslval $standard dim2` ; Y=`echo "$Y 2 - p" | dc -`
Z=`${FSLDIR}/bin/fslval $standard dim3` ; Z=`echo "$Z 2 - p" | dc -`

# first do masking, if requested
if [ $mask -lt 3 ] ; then
    if [ $mask = 1 ] ; then
	${FSLDIR}/bin/fslmaths $standard -mul 0 -add 1 -roi 1 $X 1 $Y 1 $Z 0 1 ${out}_tmp_standard_mask -odt float
    else
	${FSLDIR}/bin/fslmaths $maskmask -bin ${out}_tmp_standard_mask -odt float
    fi
    ${FSLDIR}/bin/flirt -ref $in -in ${out}_tmp_standard_mask -o ${out}_tmp_standard_mask_to_in -applyxfm -init ${out}_tmp_to_std_inv.mat
    ${FSLDIR}/bin/fslmaths ${out}_tmp_standard_mask_to_in $maskthr ${out}_tmp_standard_mask_to_in
    ${FSLDIR}/bin/fslmaths $inapply -mas ${out}_tmp_standard_mask_to_in ${out}_tmp_masked
    inapply=${out}_tmp_masked
fi

# then cut down FOV, if requested
if [ $roi -lt 3 ] ; then
    if [ $roi = 1 ] ; then
	${FSLDIR}/bin/fslmaths $standard -mul 0 -add 1 -roi 1 $X 1 $Y 1 $Z 0 1 ${out}_tmp_standard_roi -odt float
    else
	${FSLDIR}/bin/fslmaths $roimask -bin ${out}_tmp_standard_roi -odt float
    fi
    ${FSLDIR}/bin/flirt -ref $in -in ${out}_tmp_standard_roi -o ${out}_tmp_standard_roi_to_in -applyxfm -init ${out}_tmp_to_std_inv.mat
    ${FSLDIR}/bin/fslroi $inapply $out `${FSLDIR}/bin/fslstats ${out}_tmp_standard_roi_to_in -w`
else
    ${FSLDIR}/bin/imcp $inapply $out
fi

# }}}
# {{{ cleanup temporary files

if [ $debug = 0 ] ; then
    /bin/rm ${out}_tmp*
fi

# }}}