feedsRun

#! /bin/sh
#
# This script runs eddy followed by some
# tests on the output.
# It uses some b=7000 data from the pilot phase
# of the HCP. The "ground truth" is simply the
# output from eddy at a time when it seemed to
# do a good job. The tolerance is quite high. That
# reflects both that the data has a quite high
# scale (b=0 values ~2000) and also that the
# run-to-run variability of eddy is quite high
# on these data.
#

odir=$1
indir=$2
#
# Inputs 1--3 are the once neccessary for feeds to work
# Additional inputs are optional and intended for testing
# outside of the feeds context.
#
# Input 4 is alternative location of executable
#
if [ "$#" -gt 3 ]; then
    exedir=$4
   echo "Directory for eddy executables set to ${exedir}"
else
   exedir="${FSLDIR}/bin"
fi

# Find all eddy_cuda* executables
cuda_exes=""
openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
  if [ -x "${cuda_exe}" ]; then
    cuda_exes="${cuda_exes} ${cuda_exe}"
  fi
done

# Find the eddy_openmp executable
if [ -x "${exedir}/eddy_openmp" ]; then
  openmp_exe="${exedir}/eddy_openmp"
fi

if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
  echo "Cannot find any eddy executables in ${exedir}!"
  exit 1
fi

if [ ! -d "$odir" ]; then
   echo "Output directory ${odir} does not exist"
   exit 1;
fi
if [ ! -d "$indir" ]; then
   echo "Input directory ${indir} does not exist"
   exit 1;
fi

# Launch both GPU and CPU versions

cuda_jid=""
for cuda_exe in ${cuda_exes};
do
    tmp=`basename $cuda_exe`
    version=`echo $tmp | sed 's/eddy_cuda//'`
    cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyHigh_b_TestData/eddyData/testData --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --out=${odir}/eddyCudaOutput${version} --very_verbose`"
done

omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyHigh_b_TestData/eddyData/testData --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --out=${odir}/eddyOmpOutput --very_verbose`

# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
    qalter ${omp_jid} -R y
    while [ : ]; do
        for jid in ${cuda_jid};
        do
    	tmp=`qstat -j ${jid} | wc`
    	tmp=`echo $tmp | awk '{print $1}'`
    	if [ $tmp -ne 0 ]; then
    	    break
    	fi
        done
        if [ $tmp -eq 0 ]; then
    	tmp=`qstat -j ${omp_jid} | wc`
    	tmp=`echo $tmp | awk '{print $1}'`
    	if [ $tmp -eq 0 ]; then
          	    break
    	fi
        fi
        sleep 5m
    done
fi

# Check that eddy output exists

for cuda_exe in ${cuda_exes};
do
    tmp=`basename $cuda_exe`
    version=`echo $tmp | sed 's/eddy_cuda//'`
    if [ ! -f ${odir}/eddyCudaOutput${version}.nii* ]; then
	exit 1
    fi
done
if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
   exit 1
fi

# Define some constants

max_mean_ima_diff=15.0
max_max_ima_diff=20.0

# Check the results against ground truth

cuda_exit_status=0
for cuda_exe in ${cuda_exes};
do
    tmp=`basename $cuda_exe`
    version=`echo $tmp | sed 's/eddy_cuda//'`
    ./EddyHigh_b_Feeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_cuda_output` $max_mean_ima_diff $max_max_ima_diff
    cuda_exit_status=$(($cuda_exit_status + $?))
done

./EddyHigh_b_Feeds.py ${odir} Omp `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff

omp_exit_status=$?

if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
    echo "Test failed"
    exit 1
else
    echo "Test passed"
    exit 0
fi