#!/bin/sh

#   slices_summary - create summary picture from a 4D image and list of timepoints to use
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2010-2012 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 5.0 (c) 2012, 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.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
#   transferred in any form or by any means, electronic or mechanical,
#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
#   conditions of this Licence are imposed upon the receiver of the
#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.
export LC_ALL=C


Usage() {
    echo ""
    echo "Usage:"
    echo "slices_summary <4D_input> <threshold> <background_image> <pictures.sum> [-1]"
    echo "slices_summary <pictures.sum> <output.png> <space-separated list of timepoints to use; first timepoint is 0>"
    echo ""
    echo "The first usage creates the full set of summary PNG images, into a new directory <pictures.sum>"
    echo "  [-1] option: generate single-slice summary images instead of 3-slice"
    echo ""
    echo "The second usage processes the timepoint list, combining summary slices across all timepoints into a single PNG image."
    echo ""
    echo "E.g."
    echo "slices_summary groupica.ica/melodic_IC 4 $FSLDIR/data/standard/MNI152_T1_2mm groupica.ica/melodic_IC.sum"
    echo "slices_summary groupica.ica/melodic_IC.sum grot.png 5 10 0 200"
    echo ""
    exit 1
}

[ "$3" = "" ] && Usage

if [ _$FSLDIR = _ ] ; then
    FSLDIR=/usr/local/fsl
    export FSLDIR
fi

if [ `${FSLDIR}/bin/imtest $1` = 1 ] ; then

########################################################
# first usage
########################################################

  in=`${FSLDIR}/bin/remove_ext $1`
  if [ `${FSLDIR}/bin/imtest $in` = 0 ] ; then
    echo "Input image $in not found"
    Usage
  fi
  lthresh=$2
  bg=$3
  if [ `${FSLDIR}/bin/imtest $bg` = 0 ] ; then
    echo "Background image $bg not found"
    Usage
  fi
  out=$4

  allthree=1
  if [ _$5 = _-1 ] ; then
    echo "Generating single-slice summary images instead of 3-slice"
    allthree=0
  fi

  mkdir -p $out
  ${FSLDIR}/bin/imcp $bg ${out}/BG

  bgdimx=`${FSLDIR}/bin/fslval $bg dim1`
  bgdimy=`${FSLDIR}/bin/fslval $bg dim2`
  bgrange=`${FSLDIR}/bin/fslstats $bg -l 0.01 -r`

  uthresh=`${FSLDIR}/bin/fslstats $in -l 0.01 -P 50`
  uthresh=`${FSLDIR}/bin/fslstats $in -l $uthresh -P 99.9`
  echo "Upper threshold is $uthresh"

  ${FSLDIR}/bin/fslsplit $in ${out}/vol
  cd $out
  for grot in `${FSLDIR}/bin/imglob vol*` ; do
    DD=`echo $grot | awk -F vol '{print $2}'`
    fslecho  "[$DD \c"
    ${FSLDIR}/bin/fslsplit $grot grot_ -z
    /bin/rm -f grot.txt
    for g in `${FSLDIR}/bin/imglob grot_*` ; do
      ${FSLDIR}/bin/cluster -i $g -t $lthresh --osize=grot --no_table
      ${FSLDIR}/bin/fslmaths grot -sqrt -recip -mul $g -Xmean -Ymean grot -odt float
      echo "$g `${FSLDIR}/bin/fslstats grot -m`" >> grot.txt
    done

    best=`cat grot.txt | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
    nbest=`${FSLDIR}/bin/remove_ext $best | awk -F _ '{print $2}'`
    ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nbest 1
    ${FSLDIR}/bin/overlay 0 0 grot $bgrange $best $lthresh $uthresh grotB
    fslecho "$nbest\c"

    if [ $allthree = 1 ] ; then
      lbest=`echo "$nbest 4 - p" | dc -`
      if [ $lbest -lt 1 ] ; then lbest=1; fi;
      lbest=`cat grot.txt | head -n $lbest | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
      nlbest=`${FSLDIR}/bin/remove_ext $lbest | awk -F _ '{print $2}'`
      ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nlbest 1
      ${FSLDIR}/bin/overlay 0 0 grot $bgrange $lbest $lthresh $uthresh grotC
  
      ubest=`echo "$nbest 6 + p" | dc -`
      if [ $ubest -gt `cat grot.txt | wc -l` ] ; then ubest=`cat grot.txt | wc -l`; fi;
      ubest=`cat grot.txt | tail -n +$ubest | sort -k 2 -n | tail -n 1 | awk '{print $1}'`
      nubest=`${FSLDIR}/bin/remove_ext $ubest | awk -F _ '{print $2}'`
      ${FSLDIR}/bin/fslroi BG grot 0 $bgdimx 0 $bgdimy $nubest 1
      ${FSLDIR}/bin/overlay 0 0 grot $bgrange $ubest $lthresh $uthresh grotA

      fslecho  ",$nlbest,$nubest\c"
      fslmerge -y grotB grotA grotB grotC
    fi
    fslecho  "] \c"

    ${FSLDIR}/bin/slicer grotB -u -z 0 `zeropad $DD 4`.png
  done
  /bin/rm -f grot* vol* BG*
  echo ""

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

else

########################################################
# second usage
########################################################

  in=$1
  out=$2
  shift 2
  thestring="pngappend"
  while [ _$2 != _ ] ; do
    s=$1
    shift
    thestring="$thestring ${in}/`${FSLDIR}/bin/zeropad $s 4`.png +"
  done
  s=$1
  thestring="$thestring ${in}/`${FSLDIR}/bin/zeropad $s 4`.png $out"
  $thestring

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

fi

