diff --git a/EddyHigh_b_Test/feedsRun b/EddyHigh_b_Test/feedsRun
index 552c8cf106e0aba8e6a284a66711920f6eb75945..ec81bcdae0e4b75fda98cdaf6c86a2636f56e6fc 100755
--- a/EddyHigh_b_Test/feedsRun
+++ b/EddyHigh_b_Test/feedsRun
@@ -3,7 +3,7 @@
# 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
+# 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
@@ -26,33 +26,41 @@ if [ "$#" -gt 3 ]; then
echo "Directory for eddy executables set to ${exedir}"
else
exedir="${FSLDIR}/bin"
-fi
+fi
+# Find all eddy_cuda* executables
+cuda_exes=""
+openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
- if [ ! -x "$cuda_exe" ]; then
- echo "No executable ${exedir}/eddy_cuda* exists"
- exit 1
- fi
+ if [ -x "${cuda_exe}" ]; then
+ cuda_exes="${cuda_exes} ${cuda_exe}"
+ fi
done
-if [ ! -x "${exedir}/eddy_openmp" ]; then
- echo "Executable ${exedir}/eddy_openmp does not exist"
- exit 1
+
+# Find the eddy_openmp executable
+if [ -x "${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"
+ echo "Output directory ${odir} does not exist"
exit 1;
fi
if [ ! -d "$indir" ]; then
- echo "Input directory ${indir} does not exist"
+ echo "Input directory ${indir} does not exist"
exit 1;
fi
# Launch both GPU and CPU versions
cuda_jid=""
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -60,33 +68,35 @@ do
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`
-# Ensure that slots are being reserved on the queue
-qalter ${omp_jid} -R y
-
-# Wait until they have both finished
-
-while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
+
+# If running on a cluster, ensure that
+# slots are being reserved on the queue,
+# and wait until all jobs have finished
+if [ ! -z "${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
- 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 ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -106,7 +116,7 @@ max_max_ima_diff=20.0
# Check the results against ground truth
cuda_exit_status=0
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
diff --git a/EddyLSRTest/feedsRun b/EddyLSRTest/feedsRun
index e7672ee71da02e649e361f976ea394e0310e079c..c70abeec4bc43f110fcb8ec32ba587bbd2e7167c 100755
--- a/EddyLSRTest/feedsRun
+++ b/EddyLSRTest/feedsRun
@@ -4,8 +4,8 @@
# tests on the output.
# It uses some data from the pilot phase
# of the HCP where each diffusion direction was
-# scanned twice with opposing PE-directions.
-# The "ground truth" is simply the output from eddy
+# scanned twice with opposing PE-directions.
+# The "ground truth" is simply the output from eddy
# prior to Armadillo and NewNewimage.
#
@@ -23,33 +23,41 @@ if [ "$#" -gt 3 ]; then
echo "Directory for eddy executables set to ${exedir}"
else
exedir="${FSLDIR}/bin"
-fi
+fi
+# Find all eddy_cuda* executables
+cuda_exes=""
+openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
- if [ ! -x "$cuda_exe" ]; then
- echo "No executable ${exedir}/eddy_cuda* exists"
- exit 1
- fi
+ if [ -x "${cuda_exe}" ]; then
+ cuda_exes="${cuda_exes} ${cuda_exe}"
+ fi
done
-if [ ! -x "${exedir}/eddy_openmp" ]; then
- echo "Executable ${exedir}/eddy_openmp does not exist"
- exit 1
+
+# Find the eddy_openmp executable
+if [ -x "${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"
+ echo "Output directory ${odir} does not exist"
exit 1;
fi
if [ ! -d "$indir" ]; then
- echo "Input directory ${indir} does not exist"
+ echo "Input directory ${indir} does not exist"
exit 1;
fi
# Launch both GPU and CPU versions
cuda_jid=""
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -57,33 +65,36 @@ do
done
omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyLSRTestData/eddyData/testData --mask=${indir}/EddyLSRTestData/eddyData/testMask --bvals=${indir}/EddyLSRTestData/eddyData/testBvals --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs --index=${indir}/EddyLSRTestData/eddyData/testIndex --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams --topup=${indir}/EddyLSRTestData/eddyData/testTopup --out=${odir}/eddyOmpOutput --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`
-# Ensure that slots are being reserved on the queue
-qalter ${omp_jid} -R y
-
-# Wait until they have both finished
-
-while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
+
+# If running on a cluster, ensure that
+# slots are being reserved on the queue,
+# and wait until all jobs have finished
+if [ ! -z "${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
- 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 ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -103,7 +114,7 @@ max_max_ima_diff=20.0
# Check the results against ground truth
cuda_exit_status=0
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -111,7 +122,7 @@ do
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./EddyLSRFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
+./EddyLSRFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
omp_exit_status=$?
diff --git a/EddyMBSTest/feedsRun b/EddyMBSTest/feedsRun
index b58157a3fa9b544294a8d65d79e32ccf305bc6c5..00fca937a74698e8bf77a2c5733bdd97a583820b 100755
--- a/EddyMBSTest/feedsRun
+++ b/EddyMBSTest/feedsRun
@@ -1,16 +1,16 @@
#! /bin/sh
#
-# This script runs eddy for testing the
+# This script runs eddy for testing the
# movement-by-susceptibility functionality
# followed by some tests on the output.
# It uses simulated data supplied by Mark
# Graham, UCL.
-# The data is a subset of that used for
+# The data is a subset of that used for
# the MBS paper. We don't have an "actual"
# ground truth so instead we compare against
# the results from the paper (calculated with
# the Cuda version).
-# The actual data used for the test is
+# The actual data used for the test is
# .../SecondSetOfSimulations/ap/ec-volumetric-3x/images_SNR40_1
#
@@ -28,26 +28,34 @@ if [ "$#" -gt 3 ]; then
echo "Directory for eddy executables set to ${exedir}"
else
exedir="${FSLDIR}/bin"
-fi
+fi
+# Find all eddy_cuda* executables
+cuda_exes=""
+openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
- if [ ! -x "$cuda_exe" ]; then
- echo "No executable ${exedir}/eddy_cuda* exists"
- exit 1
- fi
+ if [ -x "${cuda_exe}" ]; then
+ cuda_exes="${cuda_exes} ${cuda_exe}"
+ fi
done
-if [ ! -x "${exedir}/eddy_openmp" ]; then
- echo "Executable ${exedir}/eddy_openmp does not exist"
- exit 1
+
+# Find the eddy_openmp executable
+if [ -x "${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"
+ echo "Output directory ${odir} does not exist"
exit 1;
fi
if [ ! -d "$indir" ]; then
- echo "Input directory ${indir} does not exist"
+ echo "Input directory ${indir} does not exist"
exit 1;
fi
@@ -61,7 +69,7 @@ max_max_ima_diff=0.6
# Launch both GPU and CPU versions
cuda_jid=""
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -69,33 +77,35 @@ do
done
omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyMBSTestData/eddyData/testData --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams --mask=${indir}/EddyMBSTestData/eddyData/testMask --index=${indir}/EddyMBSTestData/eddyData/testIndex --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs --bvals=${indir}/EddyMBSTestData/eddyData/testBvals --topup=${indir}/EddyMBSTestData/eddyData/testTopup --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 --flm=quadratic --dont_peas --estimate_move_by_susceptibility --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --out=${odir}/eddyOmpOutput --very_verbose`
-# Ensure that slots are being reserved on the queue
-qalter ${omp_jid} -R y
-
-# Wait until they have both finished
-
-while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
+
+# If running on a cluster, ensure that
+# slots are being reserved on the queue,
+# and wait until all jobs have finished
+if [ ! -z "${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
- 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 ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -110,15 +120,15 @@ fi
# Check the results against precomputed results
cuda_exit_status=0
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
- ./MoveBySuscFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyCudaOutput${version}.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
+ ./MoveBySuscFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyCudaOutput${version}.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./MoveBySuscFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyOmpOutput.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
+./MoveBySuscFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyOmpOutput.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
omp_exit_status=$?
diff --git a/EddyS2VTest/feedsRun b/EddyS2VTest/feedsRun
index 49863ebd8dff9f091eb0de6ef62e1edadf918691..f1dc7b769feead541075182f3e3c0b9c826da7c4 100755
--- a/EddyS2VTest/feedsRun
+++ b/EddyS2VTest/feedsRun
@@ -24,33 +24,41 @@ if [ "$#" -gt 3 ]; then
echo "Directory for eddy executables set to ${exedir}"
else
exedir="${FSLDIR}/bin"
-fi
+fi
+# Find all eddy_cuda* executables
+cuda_exes=""
+openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
- if [ ! -x "$cuda_exe" ]; then
- echo "No executable ${exedir}/eddy_cuda* exists"
- exit 1
- fi
+ if [ -x "${cuda_exe}" ]; then
+ cuda_exes="${cuda_exes} ${cuda_exe}"
+ fi
done
-if [ ! -x "${exedir}/eddy_openmp" ]; then
- echo "Executable ${exedir}/eddy_openmp does not exist"
- exit 1
+
+# Find the eddy_openmp executable
+if [ -x "${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"
+ echo "Output directory ${odir} does not exist"
exit 1;
fi
if [ ! -d "$indir" ]; then
- echo "Input directory ${odir} does not exist"
+ echo "Input directory ${odir} does not exist"
exit 1;
fi
# Launch both GPU and CPU versions
-
+
cuda_jid=""
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -58,33 +66,35 @@ do
done
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
-
-# Wait until they have both finished
-
-while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
+
+# If running on a cluster, ensure that
+# slots are being reserved on the queue,
+# and wait until all jobs have finished
+if [ ! -z "${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
- 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 ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -112,19 +122,19 @@ max_false_neg=10
# Check the results against ground truth
cuda_exit_status=0
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
echo "./S2VFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension $\
{indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCudaOutput${version}.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyCudaO\
utput${version}.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}"
- ./S2VFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCudaOutput${version}.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyCudaOutput${version}.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}
+ ./S2VFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCudaOutput${version}.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyCudaOutput${version}.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}
cuda_exit_status=$(($cuda_exit_status + $?))
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}
+./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} ${max_rot_diff}
omp_exit_status=$?
diff --git a/EddyTest/feedsRun b/EddyTest/feedsRun
index 3fd56680cd8b57c536eb3210c97b6c03e74b85db..af955aea4e3d0507f481f9265f23b3096a728c9b 100755
--- a/EddyTest/feedsRun
+++ b/EddyTest/feedsRun
@@ -1,4 +1,4 @@
-#! /bin/sh
+#!/bin/sh
#
# This script runs eddy followed by some
# tests on the output.
@@ -22,26 +22,34 @@ if [ "$#" -gt 3 ]; then
echo "Directory for eddy executables set to ${exedir}"
else
exedir="${FSLDIR}/bin"
-fi
+fi
+# Find all eddy_cuda* executables
+cuda_exes=""
+openmp_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
- if [ ! -x "$cuda_exe" ]; then
- echo "No executable ${exedir}/eddy_cuda* exists"
- exit 1
- fi
+ if [ -x "${cuda_exe}" ]; then
+ cuda_exes="${cuda_exes} ${cuda_exe}"
+ fi
done
-if [ ! -x "${exedir}/eddy_openmp" ]; then
- echo "Executable ${exedir}/eddy_openmp does not exist"
- exit 1
+
+# Find the eddy_openmp executable
+if [ -x "${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"
+ echo "Output directory ${odir} does not exist"
exit 1;
fi
if [ ! -d "$indir" ]; then
- echo "Input directory ${indir} does not exist"
+ echo "Input directory ${indir} does not exist"
exit 1;
fi
@@ -57,7 +65,7 @@ allowed_false_negatives=1
# Launch both GPU and CPU versions
cuda_jid=""
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -65,34 +73,36 @@ do
done
omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyTestData/eddyData/testData --mask=${indir}/EddyTestData/eddyData/testMask --bvals=${indir}/EddyTestData/eddyData/testBvals --bvecs=${indir}/EddyTestData/eddyData/testBvecs --index=${indir}/EddyTestData/eddyData/testIndex --acqp=${indir}/EddyTestData/eddyData/testAcqparams --repol --fwhm=10,0,0,0,0 --out=${odir}/eddyOmpOutput --dfields -v`
-# Ensure that slots are being reserved on the queue
-qalter ${omp_jid} -R y
-
-# Wait until they have both finished
-
-while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
+
+# If running on a cluster, ensure that
+# slots are being reserved on the queue,
+# and wait until all jobs have finished
+if [ ! -z "${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
- 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 ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
@@ -107,15 +117,15 @@ fi
# Check the results against ground truth
cuda_exit_status=0
-for cuda_exe in ${exedir}/eddy_cuda*;
+for cuda_exe in ${cuda_exes};
do
tmp=`basename $cuda_exe`
version=`echo $tmp | sed 's/eddy_cuda//'`
- ./EddyFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCudaOutput${version}.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyCudaOutput${version}.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
+ ./EddyFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCudaOutput${version}.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyCudaOutput${version}.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./EddyFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyOmpOutput.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyOmpOutput.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
+./EddyFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyOmpOutput.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyOmpOutput.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
omp_exit_status=$?
if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then