#!/bin/sh

#   Copyright (C) 2010-2012 University of Oxford
#
#   Stamatios Sotiropoulos
#   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_NUMERIC=C

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: qboot_parallel <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 ""
    echo " You can pass on qboot options"
    echo " Default qboot options are utilised otherwise"
    echo " For example:  qboot_parallel <subject directory> --lmax=6 --lambda=0.006"
    echo " Type 'qboot --help' for a list of available options "
    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

shift
opts="$*"

#check that all required files exist

if [ ! -d $subjdir ]; then
	echo "subject directory $subjdir 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 qboot directory structure

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

echo Queuing preprocessing stages
preprocid=`${FSLDIR}/bin/fsl_sub -T 60 -N qboot_preproc -l ${subjdir}.qboot/logs ${FSLDIR}/bin/qboot_preproc.sh ${subjdir}`


echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.qboot/commands.txt ] && rm ${subjdir}.qboot/commands.txt

 slice=0
 while [ $slice -lt $nslices ]
   do
    slicezp=`$FSLDIR/bin/zeropad $slice 4`
    if [ `$FSLDIR/bin/imtest ${subjdir}.qboot/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ];then
	echo "slice $slice has already been processed"
    else
	echo "${FSLDIR}/bin/qboot --data=${subjdir}/data_slice_${slicezp} --mask=${subjdir}/nodif_brain_mask_slice_${slicezp} -b ${subjdir}/bvals -r ${subjdir}/bvecs --forcedir --logdir=$subjdir.qboot/diff_slices/data_slice_${slicezp} ${opts}" >> ${subjdir}.qboot/commands.txt
    fi
    slice=$(($slice + 1))
 done
    
 qbootid=`${FSLDIR}/bin/fsl_sub -q long.q -j $preprocid -l ${subjdir}.qboot/logs -N qboot -t ${subjdir}.qboot/commands.txt`

 echo Queuing post processing stage
 mergeid=`${FSLDIR}/bin/fsl_sub -j $qbootid -T 60 -N qboot_postproc -l ${subjdir}.qboot/logs ${FSLDIR}/bin/qboot_postproc.sh $subjdir`
