#!/bin/sh

#   updatefeatreg
#
#   Mark Jenkinson & Steve Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2008 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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#   FMRIB Software Library, Release 4.0 (c) 2007, The University of
#   Oxford (the "Software")
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usage() {
  echo "Usage: `basename $0` <feat_directory> [-pngs]"
  echo "   Updates all inverse and concatenated transforms in a first-level"
  echo "        FEAT run, as well as the images in the FEAT report,"
  echo "        based on the fundamental registration matrices:"
  echo "          i.e. example_func2highres.mat , highres2standard.mat"
  echo "        This allows for manual/other correction of the registrations"
}

regupdate() {
    if [ -f ${1}2${2}.mat ] && [ -f ${2}2${3}.mat ] ; then
	echo concatenating ${1}2${2}.mat and ${2}2${3}.mat
	${FSLDIR}/bin/convert_xfm -omat ${1}2${3}.mat -concat ${2}2${3}.mat ${1}2${2}.mat
    fi
}

invupdate() {
    if [ -f ${1}.mat ] ; then
	a=`echo $1 | awk -F 2 '{print $1}'`
	b=`echo $1 | awk -F 2 '{print $2}'`
	echo inverting ${1}.mat
	${FSLDIR}/bin/convert_xfm -inverse -omat ${b}2${a}.mat ${1}.mat
    fi
}

picupdate() {
    if [ `${FSLDIR}/bin/imtest $1` = 1 ] && [ `${FSLDIR}/bin/imtest $2` = 1 ] && [ -f ${1}2${2}.mat ] ; then
	out=${1}2${2}
	echo creating summary picture for ${out}
	if [ $1 = "example_func" ] && [ $2 = "standard" ] && [ `${FSLDIR}/bin/imtest highres2standard_warp` = 1 ] ; then
	    ${FSLDIR}/bin/applywarp --ref=$2 --in=$1 --out=$out --warp=highres2standard_warp --premat=${1}2highres.mat
	elif [ $1 = "highres" ] && [ $2 = "standard" ] && [ `${FSLDIR}/bin/imtest highres2standard_warp` = 1 ] ; then
	    ${FSLDIR}/bin/applywarp --ref=$2 --in=$1 --out=$out --warp=highres2standard_warp
	else
	    ${FSLDIR}/bin/flirt -ref $2 -in $1 -out $out -applyxfm -init ${out}.mat
	fi
	${FSLDIR}/bin/slicer $out $2 -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
	${FSLDIR}/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ${out}1.png
	${FSLDIR}/bin/slicer $2 $out -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png
	${FSLDIR}/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png ${out}2.png
	${FSLDIR}/bin/pngappend ${out}1.png - ${out}2.png ${out}.png
	/bin/rm sl?.png
    fi
}


dirnm=$1

if [ X${dirnm}X = XX ] ; then
  usage 
  exit 1;
fi

if [ X${dirnm}X = X.X ] ; then
  dirnm=`pwd`;
fi

if [ ! -d $dirnm ] ; then
  usage 
  echo " "
  echo "$dirnm is not a valid directory"
  exit -1
fi

cd ${dirnm}/reg

regupdate example_func initial_highres highres
regupdate example_func highres standard

invupdate example_func2initial_highres
invupdate initial_highres2highres
invupdate example_func2highres
invupdate highres2standard
invupdate example_func2standard

picupdate example_func initial_highres
picupdate initial_highres highres
picupdate example_func highres
picupdate highres standard
picupdate example_func standard

