randomise_parallel

#!/bin/sh
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FSL_SUB=/usr/share/fsl/overlay/fsl_sub

export LC_ALL=C
if [ $# -le 3 ] ; then
  echo "$0 <randomise options>"
  echo ""
  echo "Actual number of permutations performed may differ slightly from those 
  requested due to tasking an equal number of permutations per fragment."
  echo ""
  echo "Caution: if a design has less unique permutations than those requested, 
  the defragment script will not work correctly!"
  exit 1
fi

RANDOMISE_OUTPUT=`$FSLDIR/bin/randomise $@ -Q`
if [ $? != 0 ] ; then 
  echo "ERROR: Randomise could not succesfully initialise with the command line given. Submission aborted."
  exit 1
fi 

PERMS=`echo $RANDOMISE_OUTPUT | awk '{print $1}'`
CONTRASTS=`echo $RANDOMISE_OUTPUT | awk '{print $2}'`
ROOTNAME=`echo $RANDOMISE_OUTPUT | awk '{print $3}'`
BASENAME=`basename $ROOTNAME`
DIRNAME=`dirname $ROOTNAME`

mkdir -p ${DIRNAME}/${BASENAME}_logs

PERMS_PER_SLOT=`echo $RANDOMISE_OUTPUT | awk '{print $4}'`
if [ x${REQUESTED_TIME} = 'x' ] ; then
    REQUESTED_TIME=30
fi

SLOTS_PER_CONTRAST=`expr $PERMS / $PERMS_PER_SLOT`

if [ $SLOTS_PER_CONTRAST -lt 1 ] ; then
    SLOTS_PER_CONTRAST=1
fi

PERMS_PER_CONTRAST=`expr $PERMS_PER_SLOT \* $SLOTS_PER_CONTRAST`

REQUESTED_SLOTS=`expr $CONTRASTS \* $SLOTS_PER_CONTRAST`

CORRECTED_PERMS=`expr $PERMS_PER_CONTRAST - $SLOTS_PER_CONTRAST`
CORRECTED_PERMS=`expr $CORRECTED_PERMS + 1`

echo "Generating" $REQUESTED_SLOTS "fragments for " $CONTRASTS " contrasts with " $PERMS_PER_SLOT "permutations per fragment. Allocating" ${REQUESTED_TIME} "minutes per fragment." 
echo "The total number of permutations per contrast will be" $PERMS_PER_CONTRAST "."

#stage 1:
CURRENT_SEED=1
if [ -e ${DIRNAME}/${BASENAME}.generate ] ; then
  /bin/rm ${DIRNAME}/${BASENAME}.generate
fi
while [ $CURRENT_SEED -le $SLOTS_PER_CONTRAST ] ; do
  SLEEPTIME=`expr 1 \* $CURRENT_SEED`
  CURRENT_CONTRAST=1
  while [ $CURRENT_CONTRAST -le $CONTRASTS ] ; do
      echo "FSLOUTPUTTYPE=NIFTI_GZ; sleep $SLEEPTIME ; ${FSLDIR}/bin/randomise $@ -n $PERMS_PER_SLOT -o ${ROOTNAME}_SEED${CURRENT_SEED} --seed=$CURRENT_SEED --skipTo=$CURRENT_CONTRAST" >> ${DIRNAME}/${BASENAME}.generate
      CURRENT_CONTRAST=`expr $CURRENT_CONTRAST + 1`
  done
  echo done $CURRENT_SEED
  CURRENT_SEED=`expr $CURRENT_SEED + 1`
done
$FSL_SUB -T ${REQUESTED_TIME} -N ${BASENAME}.generate -l ${DIRNAME}/${BASENAME}_logs/ -t ${DIRNAME}/${BASENAME}.generate -B

#stage2:
cat <<combineScript > ${DIRNAME}/${BASENAME}.defragment
#!/bin/bash
echo "Merging stat images"
for FIRSTSEED in ${ROOTNAME}_SEED1_*_p_*.nii.gz ${ROOTNAME}_SEED1_*_corrp_*.nii.gz ; do 
  ADDCOMMAND=""
  ACTIVESEED=1
  if [ -e \$FIRSTSEED ] ; then
    while [ \$ACTIVESEED -le $SLOTS_PER_CONTRAST ] ; do
      ADDCOMMAND=\`echo \$ADDCOMMAND -add \${FIRSTSEED/_SEED1_/_SEED\${ACTIVESEED}_}\`
      ACTIVESEED=\`expr \$ACTIVESEED + 1\`
    done
    ADDCOMMAND=\${ADDCOMMAND#-add}
    echo \$ADDCOMMAND
    \$FSLDIR/bin/fslmaths \$ADDCOMMAND -mul $PERMS_PER_SLOT -div $CORRECTED_PERMS \${FIRSTSEED/_SEED1/}
  fi
done

echo "Merging text files"
for FIRSTSEED in ${ROOTNAME}_SEED1_*perm_*.txt ${ROOTNAME}_SEED1_*_p_*.txt ${ROOTNAME}_SEED1_*_corrp_*.txt ; do 
  ACTIVESEED=1
  if [ -e \$FIRSTSEED ] ; then
    while [ \$ACTIVESEED -le $SLOTS_PER_CONTRAST ] ; do
      if [ \$ACTIVESEED -eq 1 ] ; then
         cat \${FIRSTSEED/_SEED1_/_SEED\${ACTIVESEED}_} >> \${FIRSTSEED/_SEED1/}
      else
         tail -n +2 \${FIRSTSEED/_SEED1_/_SEED\${ACTIVESEED}_} >> \${FIRSTSEED/_SEED1/}
      fi 
      ACTIVESEED=\`expr \$ACTIVESEED + 1\`
    done
  fi
done

echo "Renaming raw stats"
for TYPE in _ _tfce_ ; do
  for FIRSTSEED in ${ROOTNAME}_SEED1\${TYPE}tstat*.nii.gz ${ROOTNAME}_SEED1\${TYPE}fstat*.nii.gz ; do 
    if [ -e \$FIRSTSEED ] ; then
      cp \$FIRSTSEED \${FIRSTSEED/_SEED1/}
    fi
  done
done

ACTIVESEED=1
while [ \$ACTIVESEED -le $SLOTS_PER_CONTRAST ] ; do
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*_p_*
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*_corrp_*
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*stat????.nii.gz
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*stat???.nii.gz
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*stat??.nii.gz
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}*stat?.nii.gz
  rm -rf ${ROOTNAME}_SEED\${ACTIVESEED}_*perm_*.txt ${ROOTNAME}_SEED\${ACTIVESEED}_*_p_*.txt ${ROOTNAME}_SEED\${ACTIVESEED}_*_corrp_*.txt

  ACTIVESEED=\`expr \$ACTIVESEED + 1\`
done
 
echo "Done"
combineScript
chmod +x ${DIRNAME}/${BASENAME}.defragment

DEFRAGMENT_TIME=20
if [ ${REQUESTED_SLOTS} -ge 150 ] ; then
  DEFRAGMENT_TIME=40
fi

echo "${DIRNAME}/${BASENAME}.defragment" > ${DIRNAME}/${BASENAME}.command
$FSL_SUB -T ${DEFRAGMENT_TIME} -l ${DIRNAME}/${BASENAME}_logs/ -N ${BASENAME}.defragment -t ${DIRNAME}/${BASENAME}.command