#!/bin/sh

#   Copyright (C) 2004 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.
#   
#   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/1112.

if [ "x$SGE_ROOT" = "x" ] ; then
    if [ -f /usr/local/share/sge/default/common/settings.sh ] ; then
	. /usr/local/share/sge/default/common/settings.sh
    elif [ -f /usr/local/sge/default/common/settings.sh ] ; then
	. /usr/local/sge/default/common/settings.sh
    fi
fi

Usage() {
    echo ""
    echo "Usage: bedpostx <subject directory> [options]"
    echo ""
    echo "expects to find bvals and bvecs in subject directory"
    echo "expects to find data and nodif_brain_mask in subject directory"
    echo "options:"
    echo "-n (number of fibres per voxel, default 2)"
    echo "-w (ARD weight, more weight means less fibres killed per voxel, default 1)"
    echo "-b (burnin period, default 1000)"
    echo "-j (number of jumps, default 1250)"
    echo "-s (sample every, default 25)"
    echo ""
    exit 1
}

make_absolute(){
    dir=$1;
    if [ -d ${dir} ]; then
	OLDWD=`pwd`
	cd ${dir}
	dir_all=`pwd`
	cd $OLDWD
    else
	dir_all=${dir}
    fi
    echo ${dir_all}
}

[ "$1" = "" ] && Usage

subjdir=`make_absolute $1`
subjdir=`echo $subjdir | sed 's/\/$/$/g'`

echo subjectdir is $subjdir

#parse option arguments
nfibres=2
fudge=1
burnin=1000
njumps=1250
sampleevery=25
while [ ! -z "$2" ]
do
  case "$2" in
      -n) nfibres=$3;shift;;
      -w) fudge=$3;shift;;
      -b) burnin=$3;shift;;
      -j) njumps=$3;shift;;
      -s) sampleevery=$3;shift;;
      *) break;;
  esac
  shift
done

#check that all required files exist

if [ ! -d $subjdir ]; then
	echo "subject directory $1 not found"
	exit 1
fi

if [ ! -e ${subjdir}/bvecs ]; then
	echo "${subjdir}/bvecs not found"
	exit 1
fi

if [ ! -e ${subjdir}/bvals ]; then
	echo "${subjdir}/bvals not found"
	exit 1
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
	echo "${subjdir}/data not found"
	exit 1
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
	echo "${subjdir}/nodif_brain_mask not found"
	exit 1
fi

echo Making bedpostx directory structure

mkdir -p ${subjdir}.bedpostX/
mkdir -p ${subjdir}.bedpostX/diff_slices
mkdir -p ${subjdir}.bedpostX/logs
mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
mkdir -p ${subjdir}.bedpostX/xfms

mailto=`whoami`@fmrib.ox.ac.uk
echo Queuing preprocessing stages
preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -m as -N bpx_preproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`

echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
if [ "x$SGE_ROOT" = "x" ]; then
# 
# Need to set off a backgrounded monitoring task
# 
    cat <<EOM > ${subjdir}.bedpostX/monitor
#!/bin/sh
finished=0
logdir=${subjdir}.bedpostX/logs
while [ \$finished -eq 0 ] ; do
    nfin=0
    if [ -f \$logdir/bedpostx.o*.1 ] ; then
      nfin=\`cat \$logdir/bedpostx.o* |\
        grep Done | wc -w | awk '{print \$1}'\` 
    fi
    if [ \$nfin -eq $nslices ] ; then
        finished=1
    fi

    echo "\$nfin slices processed"
    sleep 600;
done
EOM
    chmod +x ${subjdir}.bedpostX/monitor
    ${subjdir}.bedpostX/monitor&
    monitorpid=$!
fi
slice=0
while [ $slice -le $nslices ]
do
    echo "${FSLDIR}/bin/my_bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $njumps $sampleevery $slice" \
	>> ${subjdir}.bedpostX/commands.txt
    slice=$(($slice + 1))
done
bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
[ "x$SGE_ROOT" = "x" ] && kill $monitorpid

echo Queuing post processing stage
mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`

if [ "x$SGE_ROOT" != "x" ]; then
    echo
    echo Type ${subjdir}.bedpostX/monitor to show progress.
    cat <<EOM > ${subjdir}.bedpostX/monitor
#!/bin/sh
finished=0
logdir=${subjdir}.bedpostX/logs
while [ \$finished -eq 0 ] ; do
    nfin=0
    if [ -f \$logdir/bedpostx.o$bedpostid.1 ] ; then
      nfin=\`cat \$logdir/bedpostx.o$bedpostid.* |\
        grep Done | wc -w | awk '{print \$1}'\` 
    fi
    if [ \$nfin -eq $nslices ] ; then
        finished=1
    fi

    echo "\$nfin slices processed"
    sleep 600;
done
EOM
    chmod +x ${subjdir}.bedpostX/monitor

    echo Type ${subjdir}.bedpostX/cancel to terminate all the queued tasks.
    cat <<EOC > ${subjdir}.bedpostX/cancel
#!/bin/sh
qdel $mergeid $bedpostid $preprocid
EOC
    chmod +x ${subjdir}.bedpostX/cancel

    echo
    echo You will get an email at the end of the post-processing stage.
    echo
fi
