possumX

#!/bin/sh

#   POSSUM
#
#   Ivana Drobnjak & Mark Jenkinson, FMRIB 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
#   
#   
#   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 Oxford
#   University Innovation ("OUI"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   Innovation@innovation.ox.ac.uk quoting reference DE/9564.
export LC_ALL=C

Usage() {
    echo ""
    echo "Usage: possumX <subject directory> [options]"
    echo ""
    echo "Subject directory needs to contain:"
    echo "1.  brain"
    echo "2.  MRpar" 
    echo "3.  motion "
    echo "4.  slcprof"
    echo "5.  pulse, pulse.info, pulse.readme, pulse.posx, pulse.posy, pulse.posz"
    echo "optional"
    echo "6.  T2"
    echo "7.  T2timecourse"
    echo "8.  b0z_dz and (in case of motion) b0x_dx, b0x_dy, ... b0z_dy"
    echo "9.  b0extra"
    echo "10. b0timecourse"
    echo ""
    echo "In case there is a cluster enviroment (e.g. SGE):"
    echo "-n (number of processors, default 1)"   
    echo "-t (estimated running time per processor (minutes), default 2000)"
    echo "-s (marix segment size [default 10000], purely for memory efficiency)"
    echo "-a (architecture [e.g., darwin or lx24-amd64])"
# tejas-add 05.11.12
    echo "-v verbose"
    echo "-j (place hold for till this job finishes)"
# tejas-end
    exit 1
}

nargs=$#
if [ $nargs -eq 0 ] ; then
  Usage
fi
# For all the users POSSUMDIR will be empty and therefore automatically become FSLDIR
# For me POSSUMDIR is my FSLDEVDIR directory. This allows me to run POSSUM on the cluster 
# without having to make it stable and wait for a day or find way to run my binaries. 
# It just seemed the easiest way to get around this. It is in all POSSUM scripts so please
# leave it that way if possible.

# tejas-edit 05.11.12
# echo "POSSUMDIR (before)" $POSSUMDIR
if [ x${POSSUMDIR} = x ] ; then
   export POSSUMDIR=$FSLDIR
fi
# echo "POSSUMDIR (after)" $POSSUMDIR

# tejas-end

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}
}

run(){
 echo "$1" >> $2/possum.com
 echo "$1" >> $2/possum.log
 date >> $2/possum.log
 $1 >> $2/possum.log 2>&1
 date >> $2/possum.log
}

subjdir=`make_absolute $1`
# tejas-edit 05.11.12
subjdir=`echo $subjdir | sed 's/\/$/$/g'` 1>/dev/null
# tejas-end
echo subjectdir is $subjdir

nproc=1
ntime=2000
segs=1000
#tejas:added option "-j" to hold jobs; secret option userf: -r
while [ ! -z "$2" ]
do
  case "$2" in
      -n) nproc=$3;shift;;
      -t) ntime=$3;shift;;
      -s) segs=$3;shift;;
      -a) arch="-a $3";shift;;
      -v) ver="-v";shift;;
      -j) holdjb="$3";shift;;
      -r) dontuserf="dontdoit";shift;;
      *) break;;
  esac
  shift
done

#check that all required files exist

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

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

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

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

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

if [ ! -e ${subjdir}/pulse.info ]; then
	echo "${subjdir}/pulse.info not found"
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/brain` -eq 0 ]; then
  if [  `${FSLDIR}/bin/imtest ${subjdir}/object` -eq 0 ]; then
	echo "could not find ${subjdir}/brain or ${subjdir}/object"
	exit 1
  else
        command="-i ${subjdir}/object"
  fi
else
  command="-i ${subjdir}/brain"
fi

command="$command -x ${subjdir}/MRpar -f ${subjdir}/slcprof -p ${subjdir}/pulse -m ${subjdir}/motion $ver "

if [ `${FSLDIR}/bin/imtest ${subjdir}/RFtrans` -eq 1 ]; then
	command="$command -s ${subjdir}/RFtrans"
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/RFrec` -eq 1 ]; then
	command="$command -r ${subjdir}/RFrec"
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/T2` -eq 1 ]; then
	command="$command -a ${subjdir}/T2 -t ${subjdir}/T2timecourse"
        if [ ! -e ${subjdir}/T2timecourse ]; then
	   echo "${subjdir}/T2timecourse not found"
        fi
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/T2_4D` -eq 1 ]; then
	command="$command -q ${subjdir}/T2_4D -u ${subjdir}/T2_4Dtimecourse"
        if [ ! -e ${subjdir}/T2_4Dtimecourse ]; then
	   echo "${subjdir}/T2_4Dtimecourse not found"
        fi
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/b0z_dz` -eq 1 ]; then
	command="$command -b ${subjdir}/b0"
fi

if [ `${FSLDIR}/bin/imtest ${subjdir}/b0extra` -eq 1 ]; then
	command="$command --b0extra=${subjdir}/b0extra --b0time=${subjdir}/b0timecourse -l 4"
	if [ ! -e ${subjdir}/b0timecourse ]; then
	   echo "${subjdir}/b0timecourse not found"
        fi
fi

if [ -e ${subjdir}/nospeedup ]; then
        command="$command --nospeedup"
fi

if [ -e ${subjdir}/kcoord.on ]; then
        command="$command -k"
fi

if [ ! -e ${subjdir}/noise ]; then
        echo "sigma" 0 > ${subjdir}/noise
fi
    
echo Making possum directory structure
mkdir -p ${subjdir}/diff_proc
mkdir -p ${subjdir}/logs
mkdir -p ${subjdir}/logs/pid_${$}
mailto=`whoami`@fmrib.ox.ac.uk

echo Preprocessing stage
echo "${POSSUMDIR}/bin/possum_matrix -p ${subjdir}/pulse -m ${subjdir}/motion --seg=$segs -o ${subjdir}/matrix"
# tejas-edit 05.11.12
${POSSUMDIR}/bin/possum_matrix -p ${subjdir}/pulse -m ${subjdir}/motion --seg=$segs -o ${subjdir}/matrix >> ${subjdir}/possum_matrix.log 2>${subjdir}/possum_matrix.err
# tejas-end

echo Processing stage 
date
command="$command --nproc=${nproc}"
[ -f ${subjdir}/possum.com ] && rm ${subjdir}/possum.com
procnum=0
if [ ! -z $dontuserf ]; then dontuserf="--rfavg";fi
while [ $procnum -lt $nproc ]
do
    echo "${POSSUMDIR}/bin/possum $command -e ${subjdir}/matrix --procid=${procnum} -o ${subjdir}/diff_proc/signal_proc_${procnum} $dontuserf" >> ${subjdir}/possum.com
    procnum=$(($procnum + 1))
done

#tejas-add
if [ ! -z $holdjb ]; then hold="-j $holdjb "; fi

echo "${FSLDIR}/bin/fsl_sub -T $ntime -l ${subjdir}/logs $arch -M $mailto -N possum -t ${subjdir}/possum.com"
unset LD_LIBRARY_PATH DYLD_LIBRARY_PATH DYLD_FALLBACK_LIBRARY_PATH
possumid=`${FSLDIR}/bin/fsl_sub -T $ntime ${hold}-l ${subjdir}/logs $arch -M $mailto -N possum -t ${subjdir}/possum.com` 
#tejas-end


echo Post processing stage
date

echo "${FSLDIR}/bin/fsl_sub -T 10 -j $possumid -F -l ${subjdir}/logs $arch ${POSSUMDIR}/bin/possumX_postproc.sh $subjdir $nproc"

mergeid=`${FSLDIR}/bin/fsl_sub -T 10 -j $possumid -F -l ${subjdir}/logs $arch ${POSSUMDIR}/bin/possumX_postproc.sh $subjdir $nproc`

## Tejas-edit 05.11.12 : CHANGE THIS!
echo "possumX-possumID $possumid"
echo "possumX-mergeID $mergeid"
## Tejas-end

echo Done
date
exit 0