Fixed script to run also OpenMP test

EddyS2VTest/feedsRun

@@ -6,10 +6,8 @@
 # Graham, UCL, which allows us to have a ground
 # truth. The data is a subset of that used
 # for the s2v paper.
-# At the time of writing this (May, 2017) the openmp version
-# is not able to do slice-to-vol realignment. Hence only
-# the cuda version is tested. The script should be updated
-# if/when there is an openmp implementation of slice-to-vol.
+# The script was updated in May 2021 to test also the openmp
+# version.
 #
 
 odir=$1
@@ -35,10 +33,10 @@ do
 	exit 1
     fi
 done
-#if [ ! -x "${exedir}/eddy_openmp" ]; then
-#   echo "Executable ${exedir}/eddy_openmp does not exist"
-#   exit 1
-#fi
+if [ ! -x "${exedir}/eddy_openmp" ]; then
+   echo "Executable ${exedir}/eddy_openmp does not exist"
+   exit 1
+fi
  
 if [ ! -d "$odir" ]; then
    echo "Output directory ${odir} does not exist" 
@@ -59,9 +57,9 @@ do
     cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --ol_nvox=500 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput${version} --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`"
 done
 
-# omp_jid=`fsl_sub -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyOmpOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyOmpOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
 # Ensure that slots are being reserved on the queue
-# qalter ${omp_jid} -R y
+qalter ${omp_jid} -R y
 
 # Wait until they have both finished
 
@@ -75,15 +73,12 @@ while [ : ]; do
 	fi
     done
     if [ $tmp -eq 0 ]; then
-	break
+	tmp=`qstat -j ${omp_jid} | wc`
+	tmp=`echo $tmp | awk '{print $1}'`
+	if [ $tmp -eq 0 ]; then
+      	    break
+	fi
     fi
-#    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
 
@@ -94,12 +89,14 @@ do
     tmp=`basename $cuda_exe`
     version=`echo $tmp | sed 's/eddy_cuda//'`
     if [ ! -f ${odir}/eddyCudaOutput${version}.nii* ]; then
+	echo "Cuda output eddyCudaOutput${version} missing"
 	exit 1
     fi
 done
-#if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
-#   exit 1
-#fi
+if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
+    echo "Omp output eddyOmpOutput missing"
+    exit 1
+fi
 
 # Define some constants
 # These are for the comparison of output images divided on b=0, b=700 and b=2000
@@ -127,6 +124,9 @@ utput${version}.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/
 done
 
 omp_exit_status=0
+./S2VFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyOmpOutput.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyOmpOutput.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}   
+omp_exit_status=$?
+
 
 if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
     echo "Test failed"