From 55fe275f6d59c42c2eeb0aed298f5114954eeed6 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 24 Nov 2021 11:08:09 +0000
Subject: [PATCH] RF: Major re-arrangement of eddy tests so that job submission
/ monitoring code is shared across all tests in a common "runEddy" script.
Also test both $FSLDIR/bin/eddy_openmp and $FSLDIR/bin/eddy_cpu if either
exist.
---
eddy/{EddyTest => }/EddyFeeds.py | 0
.../{EddyHigh_b_Test => }/EddyHigh_b_Feeds.py | 0
eddy/EddyHigh_b_Test/feedsInputs | 1 -
eddy/EddyHigh_b_Test/feedsRun | 148 ----------------
eddy/{EddyLSRTest => }/EddyLSRFeeds.py | 0
eddy/EddyLSRTest/LaunchEddy.sh | 25 ---
eddy/EddyLSRTest/feedsInputs | 1 -
eddy/EddyLSRTest/feedsRun | 146 ----------------
eddy/EddyMBSTest/feedsInputs | 1 -
eddy/EddyMBSTest/feedsRun | 151 -----------------
eddy/EddyS2VTest/feedsInputs | 1 -
eddy/EddyS2VTest/feedsRun | 158 ------------------
eddy/EddyS2VTest/rubbestad.txt | 12 --
eddy/EddyTest/feedsInputs | 1 -
eddy/EddyTest/feedsRun | 151 -----------------
eddy/{EddyMBSTest => }/MoveBySuscFeeds.py | 0
eddy/{EddyS2VTest => }/S2VFeeds.py | 0
eddy/feedsRun.EddyHigh_b_Test | 74 ++++++++
eddy/feedsRun.EddyLSRTest | 71 ++++++++
eddy/feedsRun.EddyMBSTest | 77 +++++++++
eddy/feedsRun.EddyS2VTest | 81 +++++++++
eddy/feedsRun.EddyTest | 71 ++++++++
22 files changed, 374 insertions(+), 796 deletions(-)
rename eddy/{EddyTest => }/EddyFeeds.py (100%)
rename eddy/{EddyHigh_b_Test => }/EddyHigh_b_Feeds.py (100%)
delete mode 100755 eddy/EddyHigh_b_Test/feedsInputs
delete mode 100755 eddy/EddyHigh_b_Test/feedsRun
rename eddy/{EddyLSRTest => }/EddyLSRFeeds.py (100%)
delete mode 100644 eddy/EddyLSRTest/LaunchEddy.sh
delete mode 100755 eddy/EddyLSRTest/feedsInputs
delete mode 100755 eddy/EddyLSRTest/feedsRun
delete mode 100755 eddy/EddyMBSTest/feedsInputs
delete mode 100755 eddy/EddyMBSTest/feedsRun
delete mode 100755 eddy/EddyS2VTest/feedsInputs
delete mode 100755 eddy/EddyS2VTest/feedsRun
delete mode 100644 eddy/EddyS2VTest/rubbestad.txt
delete mode 100755 eddy/EddyTest/feedsInputs
delete mode 100755 eddy/EddyTest/feedsRun
rename eddy/{EddyMBSTest => }/MoveBySuscFeeds.py (100%)
rename eddy/{EddyS2VTest => }/S2VFeeds.py (100%)
create mode 100755 eddy/feedsRun.EddyHigh_b_Test
create mode 100755 eddy/feedsRun.EddyLSRTest
create mode 100755 eddy/feedsRun.EddyMBSTest
create mode 100755 eddy/feedsRun.EddyS2VTest
create mode 100755 eddy/feedsRun.EddyTest
diff --git a/eddy/EddyTest/EddyFeeds.py b/eddy/EddyFeeds.py
similarity index 100%
rename from eddy/EddyTest/EddyFeeds.py
rename to eddy/EddyFeeds.py
diff --git a/eddy/EddyHigh_b_Test/EddyHigh_b_Feeds.py b/eddy/EddyHigh_b_Feeds.py
similarity index 100%
rename from eddy/EddyHigh_b_Test/EddyHigh_b_Feeds.py
rename to eddy/EddyHigh_b_Feeds.py
diff --git a/eddy/EddyHigh_b_Test/feedsInputs b/eddy/EddyHigh_b_Test/feedsInputs
deleted file mode 100755
index 16e9916..0000000
--- a/eddy/EddyHigh_b_Test/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-EddyHigh_b_TestData/eddyData
diff --git a/eddy/EddyHigh_b_Test/feedsRun b/eddy/EddyHigh_b_Test/feedsRun
deleted file mode 100755
index 83cb34f..0000000
--- a/eddy/EddyHigh_b_Test/feedsRun
+++ /dev/null
@@ -1,148 +0,0 @@
-#! /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=""
-cpu_exe=""
-for cuda_exe in ${exedir}/eddy_cuda*;
-do
- if [ -x "${cuda_exe}" ]; then
- cuda_exes="${cuda_exes} ${cuda_exe}"
- fi
-done
-
-# Find the eddy_cpu executable
-if [ -x "${exedir}/eddy_openmp" ]; then
- cpu_exe="${exedir}/eddy_openmp"
-fi
-
-if [ "${cuda_exes}" == "" ] && [ "${cpu_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
-
-if [ "${cpu_exe}" != "" ]; then
- cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${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=${odir}/eddyCpuOutput --very_verbose`
-fi
-
-# If running on a cluster, ensure that
-# slots are being reserved on the queue,
-# and wait until all jobs have finished
-if [ ! -z "${SGE_ROOT}" ]; then
- if [ "${cpu_exe}" != "" ]; then
- qalter ${cpu_jid} -R y
- fi
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
- if [ "${cpu_exe}" != "" ]; then
- if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${cpu_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
- 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 [ "${cpu_exe}" != "" ]; then
- if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
- echo "eddyCpuOutput missing"
- exit 1
- fi
-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 + $?))
-done
-
-cpu_exit_status=0
-if [ "${cpu_exe}" != "" ]; then
- ./EddyHigh_b_Feeds.py ${odir} Cpu `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
- cpu_exit_status=$?
-fi
-
-if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
- echo "Test failed"
- exit 1
-else
- echo "Test passed"
- exit 0
-fi
diff --git a/eddy/EddyLSRTest/EddyLSRFeeds.py b/eddy/EddyLSRFeeds.py
similarity index 100%
rename from eddy/EddyLSRTest/EddyLSRFeeds.py
rename to eddy/EddyLSRFeeds.py
diff --git a/eddy/EddyLSRTest/LaunchEddy.sh b/eddy/EddyLSRTest/LaunchEddy.sh
deleted file mode 100644
index 3bbd752..0000000
--- a/eddy/EddyLSRTest/LaunchEddy.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#! /bin/bash
-
-export exedir="/home/fs0/jesper/fsl/src/BuildingEddy_5_0_11_for_PreRelease/eddy/"
-export indir="/vols/Data/fsldev/dataSets/EddyLSRTestData/eddyData"
-export odir="/vols/Data/fsldev/dataSets/EddyLSRTestData/eddyData/Precomputed"
-
-fsl_sub -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/testData --mask=${indir}/testMask --bvals=${indir}/testBvals --bvecs=${indir}/testBvecs --index=${indir}/testIndex --acqp=${indir}/testAcqparams --topup=${indir}/testTopup --out=${odir}/eddy_openmp_output --resamp=lsr --fep --nvoxhp=5000 --dont_sep_offs_move --very_verbose
-
-fsl_sub -q cuda.q ${exedir}/eddy_cuda7.5 --imain=${indir}/testData --mask=${indir}/testMask --bvals=${indir}/testBvals --bvecs=${indir}/testBvecs --index=${indir}/testIndex --acqp=${indir}/testAcqparams --topup=${indir}/testTopup --out=${odir}/eddy_cuda_output --resamp=lsr --fep --nvoxhp=5000 --dont_sep_offs_move --very_verbose
-
-#
-# Run new eddy as well, as a kind of pre-test
-#
-
-export exedir="/home/fs0/jesper/DebugEddyNewNewimage/eddy_new/eddy"
-export indir="/vols/Data/fsldev/dataSets/EddyLSRTestData/eddyData"
-export odir="/vols/Scratch/HCP/Diffusion/jesper/EddyLSRFeedsTest20190129"
-
-fsl_sub -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/testData --mask=${indir}/testMask --bvals=${indir}/testBvals --bvecs=${indir}/testBvecs --index=${indir}/testIndex --acqp=${indir}/testAcqparams --topup=${indir}/testTopup --out=${odir}/eddy_openmp_output --resamp=lsr --fep --nvoxhp=5000 --dont_sep_offs_move --very_verbose
-
-fsl_sub -q cuda.q ${exedir}/eddy_cuda --imain=${indir}/testData --mask=${indir}/testMask --bvals=${indir}/testBvals --bvecs=${indir}/testBvecs --index=${indir}/testIndex --acqp=${indir}/testAcqparams --topup=${indir}/testTopup --out=${odir}/eddy_cuda_output --resamp=lsr --fep --nvoxhp=5000 --dont_sep_offs_move --very_verbose
-
-
-
-
diff --git a/eddy/EddyLSRTest/feedsInputs b/eddy/EddyLSRTest/feedsInputs
deleted file mode 100755
index d2c80fb..0000000
--- a/eddy/EddyLSRTest/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-EddyLSRTestData/eddyData
diff --git a/eddy/EddyLSRTest/feedsRun b/eddy/EddyLSRTest/feedsRun
deleted file mode 100755
index 4a5dad8..0000000
--- a/eddy/EddyLSRTest/feedsRun
+++ /dev/null
@@ -1,146 +0,0 @@
-#! /bin/sh
-#
-# This script runs eddy followed by some
-# 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
-# prior to Armadillo and NewNewimage.
-#
-
-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=""
-cpu_exe=""
-for cuda_exe in ${exedir}/eddy_cuda*;
-do
- if [ -x "${cuda_exe}" ]; then
- cuda_exes="${cuda_exes} ${cuda_exe}"
- fi
-done
-
-# Find the eddy_cpu executable
-if [ -x "${exedir}/eddy_openmp" ]; then
- cpu_exe="${exedir}/eddy_openmp"
-fi
-
-if [ "${cuda_exes}" == "" ] && [ "${cpu_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}/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=${odir}/eddyCudaOutput${version} --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`"
-done
-
-if [ "${cpu_exe}" != "" ]; then
- cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${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=${odir}/eddyCpuOutput --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`
-fi
-
-# If running on a cluster, ensure that
-# slots are being reserved on the queue,
-# and wait until all jobs have finished
-if [ ! -z "${SGE_ROOT}" ]; then
- if [ "${cpu_exe}" != "" ]; then
- qalter ${cpu_jid} -R y
- fi
-
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
- if [ "${cpu_exe}" != "" ]; then
- if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${cpu_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
- 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 [ "${cpu_exe}" != "" ]; then
- if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
- echo "eddyCpuOutput missing"
- exit 1
- fi
-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//'`
- ./EddyLSRFeeds.py ${odir} Cuda${version} `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCudaOutput${version}` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_cuda_output` $max_mean_ima_diff $max_max_ima_diff
- cuda_exit_status=$(($cuda_exit_status + $?))
-done
-
-cpu_exit_status=0
-if [ "${cpu_exe}" != "" ]; then
- ./EddyLSRFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
- cpu_exit_status=$?
-fi
-
-if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
- echo "Test failed"
- exit 1
-else
- echo "Test passed"
- exit 0
-fi
diff --git a/eddy/EddyMBSTest/feedsInputs b/eddy/EddyMBSTest/feedsInputs
deleted file mode 100755
index 0d13a25..0000000
--- a/eddy/EddyMBSTest/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-EddyMBSTestData/eddyData
diff --git a/eddy/EddyMBSTest/feedsRun b/eddy/EddyMBSTest/feedsRun
deleted file mode 100755
index 9be5681..0000000
--- a/eddy/EddyMBSTest/feedsRun
+++ /dev/null
@@ -1,151 +0,0 @@
-#! /bin/sh
-#
-# 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 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
-# .../SecondSetOfSimulations/ap/ec-volumetric-3x/images_SNR40_1
-#
-
-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=""
-cpu_exe=""
-for cuda_exe in ${exedir}/eddy_cuda*;
-do
- if [ -x "${cuda_exe}" ]; then
- cuda_exes="${cuda_exes} ${cuda_exe}"
- fi
-done
-
-# Find the eddy_cpu executable
-if [ -x "${exedir}/eddy_openmp" ]; then
- cpu_exe="${exedir}/eddy_openmp"
-fi
-
-if [ "${cuda_exes}" == "" ] && [ "${cpu_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
-
-# Define some constants
-
-max_mean_dfield_diff=0.03
-max_max_dfield_diff=0.06
-max_mean_ima_diff=0.3
-max_max_ima_diff=0.6
-
-# 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}/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=${odir}/eddyCudaOutput${version} --very_verbose`"
-done
-
-if [ "${cpu_exe}" != "" ]; then
- cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${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=${odir}/eddyCpuOutput --very_verbose`
-fi
-
-# If running on a cluster, ensure that
-# slots are being reserved on the queue,
-# and wait until all jobs have finished
-if [ ! -z "${SGE_ROOT}" ]; then
- if [ "${cpu_exe}" != "" ]; then
- qalter ${cpu_jid} -R y
- fi
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
- if [ "${cpu_exe}" != "" ]; then
- if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${cpu_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
- 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 [ "${cpu_exe}" != "" ]; then
- if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
- exit 1
- fi
-fi
-
-# Check the results against precomputed results
-
-cuda_exit_status=0
-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} ${max_max_dfield_diff}
- cuda_exit_status=$(($cuda_exit_status + $?))
-done
-
-cpu_exit_status=0
-if [ "${cpu_exe}" != "" ]; then
- ./MoveBySuscFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyCpuOutput.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} ${max_max_dfield_diff}
- cpu_exit_status=$?
-fi
-
-if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
- echo "Test failed"
- exit 1
-else
- echo "Test passed"
- exit 0
-fi
diff --git a/eddy/EddyS2VTest/feedsInputs b/eddy/EddyS2VTest/feedsInputs
deleted file mode 100755
index b6aff52..0000000
--- a/eddy/EddyS2VTest/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-EddyS2VTestData/eddyData
diff --git a/eddy/EddyS2VTest/feedsRun b/eddy/EddyS2VTest/feedsRun
deleted file mode 100755
index 37f6a1e..0000000
--- a/eddy/EddyS2VTest/feedsRun
+++ /dev/null
@@ -1,158 +0,0 @@
-#! /bin/sh
-#
-# This script runs eddy on data with intra-volume movement,
-# followed by some tests on the output.
-# It uses simulated data supplied by Mark
-# Graham, UCL, which allows us to have a ground
-# truth. The data is a subset of that used
-# for the s2v paper.
-# The script was updated in May 2021 to test also the openmp
-# version.
-#
-
-odir=$1
-indir=$2
-#
-# Inputs 1--3 are the ones neccessary for feeds to work
-# Additional inputs are optional and intended for testing
-# outside of the feeds context.
-#
-# Input 4 is alternative location of executable
-#
-if [ "$#" -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=""
-cpu_exe=""
-for cuda_exe in ${exedir}/eddy_cuda*;
-do
- if [ -x "${cuda_exe}" ]; then
- cuda_exes="${cuda_exes} ${cuda_exe}"
- fi
-done
-
-# Find the eddy_cpu executable
-if [ -x "${exedir}/eddy_openmp" ]; then
- cpu_exe="${exedir}/eddy_openmp"
-fi
-
-if [ "${cuda_exes}" == "" ] && [ "${cpu_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 ${odir} 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}/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
-
-if [ "${cpu_exe}" != "" ]; then
- cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${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=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCpuOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
-fi
-
-# If running on a cluster, ensure that
-# slots are being reserved on the queue,
-# and wait until all jobs have finished
-if [ ! -z "${SGE_ROOT}" ]; then
- if [ "${cpu_exe}" != "" ]; then
- qalter ${cpu_jid} -R y
- fi
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
- if [ "${cpu_exe}" != "" ]; then
- if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${cpu_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
- 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
- echo "Cuda output eddyCudaOutput${version} missing"
- exit 1
- fi
-done
-if [ "${cpu_exe}" != "" ]; then
- if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
- echo "eddyCpuOutput missing"
- exit 1
- fi
-fi
-
-# Define some constants
-# These are for the comparison of output images divided on b=0, b=700 and b=2000
-max_ima_diff="2.0 2.5 0.6 0.7 0.5 0.6"
-# Translations
-max_trans_diff="0.2 1.0"
-# Rotations
-max_rot_diff="0.2 2.0"
-# Outliers
-max_false_pos=10
-max_false_neg=10
-
-# 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//'`
- 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} ${max_rot_diff}
- cuda_exit_status=$(($cuda_exit_status + $?))
-done
-
-cpu_exit_status=0
-
-if [ "${cpu_exe}" != "" ]; then
- ./S2VFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCpuOutput.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyCpuOutput.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}
- cpu_exit_status=$?
-fi
-
-
-if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
- echo "Test failed"
- exit 1
-else
- echo "Test passed"
- exit 0
-fi
diff --git a/eddy/EddyS2VTest/rubbestad.txt b/eddy/EddyS2VTest/rubbestad.txt
deleted file mode 100644
index 3d7a911..0000000
--- a/eddy/EddyS2VTest/rubbestad.txt
+++ /dev/null
@@ -1,12 +0,0 @@
-export indir=/vols/Data/fsldev/dataSets
-export odir=/vols/Scratch/HCP/Diffusion/jesper/EddyS2VFeedsTest20190129
-exedir=/home/fs0/jesper/DebugEddyNewNewimage/eddy_new/eddy
-
-${exedir}/eddy_cuda --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 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/NewEddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose
-
-
-export indir=/vols/Data/fsldev/dataSets
-export odir=/vols/Scratch/HCP/Diffusion/jesper/EddyS2VFeedsTest20190129
-exedir=/home/fs0/jesper/fsl/src/BuildingEddyForHCP_2017_09_29/eddy
-
-${exedir}/eddy_cuda8.0 --imain=${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=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/OldEddyCudaOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose
diff --git a/eddy/EddyTest/feedsInputs b/eddy/EddyTest/feedsInputs
deleted file mode 100755
index dcfa4da..0000000
--- a/eddy/EddyTest/feedsInputs
+++ /dev/null
@@ -1 +0,0 @@
-EddyTestData/eddyData
diff --git a/eddy/EddyTest/feedsRun b/eddy/EddyTest/feedsRun
deleted file mode 100755
index cf3f1ac..0000000
--- a/eddy/EddyTest/feedsRun
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/bin/sh
-#
-# This script runs eddy followed by some
-# tests on the output.
-# It uses simulated data supplied by Mark
-# Graham, UCL, which allows us to have a ground
-# truth. The data is a subset of that used
-# for the outlier paper.
-#
-
-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=""
-cpu_exe=""
-for cuda_exe in ${exedir}/eddy_cuda*;
-do
- if [ -x "${cuda_exe}" ]; then
- cuda_exes="${cuda_exes} ${cuda_exe}"
- fi
-done
-
-# Find the eddy_cpu executable
-if [ -x "${exedir}/eddy_openmp" ]; then
- cpu_exe="${exedir}/eddy_openmp"
-fi
-
-if [ "${cuda_exes}" == "" ] && [ "${cpu_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
-
-# Define some constants
-
-max_mean_dfield_diff=0.5
-max_max_dfield_diff=1.0
-max_mean_ima_diff=1.5
-max_max_ima_diff=3.0
-allowed_false_positives=1
-allowed_false_negatives=1
-
-# 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}/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}/eddyCudaOutput${version} --dfields -v`"
-done
-
-if [ "${cpu_exe}" != "" ]; then
- cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${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}/eddyCpuOutput --dfields -v`
-fi
-
-# If running on a cluster, ensure that
-# slots are being reserved on the queue,
-# and wait until all jobs have finished
-if [ ! -z "${SGE_ROOT}" ]; then
- if [ "${cpu_exe}" != "" ]; then
- qalter ${cpu_jid} -R y
- fi
-
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
- if [ "${cpu_exe}" != "" ]; then
- if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${cpu_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
- 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 [ "${cpu_exe}" != "" ]; then
- if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
- echo "eddyCpuOutput missing"
- exit 1
- fi
-fi
-
-# 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//'`
- ./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 + $?))
-done
-
-cpu_exit_status=0
-
-if [ "${cpu_exe}" != "" ]; then
- ./EddyFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCpuOutput.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyCpuOutput.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} ${allowed_false_negatives}
- cpu_exit_status=$?
-fi
-
-if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
- echo "Test failed"
- exit 1
-else
- echo "Test passed"
- exit 0
-fi
diff --git a/eddy/EddyMBSTest/MoveBySuscFeeds.py b/eddy/MoveBySuscFeeds.py
similarity index 100%
rename from eddy/EddyMBSTest/MoveBySuscFeeds.py
rename to eddy/MoveBySuscFeeds.py
diff --git a/eddy/EddyS2VTest/S2VFeeds.py b/eddy/S2VFeeds.py
similarity index 100%
rename from eddy/EddyS2VTest/S2VFeeds.py
rename to eddy/S2VFeeds.py
diff --git a/eddy/feedsRun.EddyHigh_b_Test b/eddy/feedsRun.EddyHigh_b_Test
new file mode 100755
index 0000000..7b238aa
--- /dev/null
+++ b/eddy/feedsRun.EddyHigh_b_Test
@@ -0,0 +1,74 @@
+#! /bin/sh
+#
+# This script runs eddy followed by some
+# tests on the output.
+# It uses some b=7000 data from the pilot phase
+# of the HCP. The "ground truth" is simply the
+# output from eddy at a time when it seemed to
+# do a good job. The tolerance is quite high. That
+# reflects both that the data has a quite high
+# scale (b=0 values ~2000) and also that the
+# run-to-run variability of eddy is quite high
+# on these data.
+#
+
+set -e
+
+thisdir=$(cd $(dirname $0) && pwd)
+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
+
+if [ ! -d "$odir" ]; then
+ echo "Output directory ${odir} does not exist"
+ exit 1;
+fi
+if [ ! -d "$indir" ]; then
+ echo "Input directory ${indir} does not exist"
+ exit 1;
+fi
+
+# Prepare arguments to pass to eddy
+eddy_args="--imain=${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 --very_verbose"
+
+# run eddy
+output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
+
+# Define some constants
+max_mean_ima_diff=15.0
+max_max_ima_diff=20.0
+
+# Check the results against ground truth
+for prefix in ${output_prefixes}; do
+
+ if [[ "${prefix}" = *cuda* ]]; then
+ precomputed="${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_cuda_output"
+ else
+ precomputed="${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output"
+ fi
+
+ ${thisdir}/EddyHigh_b_Feeds.py ${odir} `basename ${prefix}` \
+ `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` \
+ `imglob -extension ${prefix}` \
+ `imglob -extension ${precomputed}` \
+ $max_mean_ima_diff $max_max_ima_diff
+done
diff --git a/eddy/feedsRun.EddyLSRTest b/eddy/feedsRun.EddyLSRTest
new file mode 100755
index 0000000..d965a57
--- /dev/null
+++ b/eddy/feedsRun.EddyLSRTest
@@ -0,0 +1,71 @@
+#! /bin/sh
+#
+# This script runs eddy followed by some
+# tests on the output.
+# It uses some data from the pilot phase
+# of the HCP where each diffusion direction was
+# scanned twice with opposing PE-directions.
+# The "ground truth" is simply the output from eddy
+# prior to Armadillo and NewNewimage.
+#
+
+set -e
+
+thisdir=$(cd $(dirname $0) && pwd)
+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
+
+if [ ! -d "$odir" ]; then
+ echo "Output directory ${odir} does not exist"
+ exit 1;
+fi
+if [ ! -d "$indir" ]; then
+ echo "Input directory ${indir} does not exist"
+ exit 1;
+fi
+
+# Prepare arguments to pass to eddy
+eddy_args="--imain=${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 " \
+ "--resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 " \
+ "--dont_peas --very_verbose"
+
+# run eddy
+output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
+
+# Define some constants
+max_mean_ima_diff=15.0
+max_max_ima_diff=20.0
+
+# Check the results against ground truth
+for prefix in ${output_prefixes}; do
+ if [[ "${prefix}" = *cuda* ]]; then
+ precomputed="${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_cuda_output"
+ else
+ precomputed="${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output"
+ fi
+
+ ${thisdir}/EddyLSRFeeds.py ${odir} `basename ${prefix}` \
+ `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` \
+ `imglob -extension ${prefix}` \
+ `imglob -extension ${precomputed}` \
+ $max_mean_ima_diff $max_max_ima_diff
+done
diff --git a/eddy/feedsRun.EddyMBSTest b/eddy/feedsRun.EddyMBSTest
new file mode 100755
index 0000000..babc78e
--- /dev/null
+++ b/eddy/feedsRun.EddyMBSTest
@@ -0,0 +1,77 @@
+#! /bin/sh
+#
+# This script runs eddy for testing the
+# movement-by-susceptibility functionality
+# followed by some tests on the output.
+# It uses simulated data supplied by Mark
+# Graham, UCL.
+# The data is a subset of that used for
+# the MBS paper. We don't have an "actual"
+# ground truth so instead we compare against
+# the results from the paper (calculated with
+# the Cuda version).
+# The actual data used for the test is
+# .../SecondSetOfSimulations/ap/ec-volumetric-3x/images_SNR40_1
+#
+
+set -e
+
+thisdir=$(cd $(dirname $0) && pwd)
+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
+
+if [ ! -d "$odir" ]; then
+ echo "Output directory ${odir} does not exist"
+ exit 1;
+fi
+if [ ! -d "$indir" ]; then
+ echo "Input directory ${indir} does not exist"
+ exit 1;
+fi
+
+# Prepare arguments to pass to eddy
+eddy_args="--imain=${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 --very_verbose"
+
+# run eddy
+output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
+
+# Define some constants
+max_mean_dfield_diff=0.03
+max_max_dfield_diff=0.06
+max_mean_ima_diff=0.3
+max_max_ima_diff=0.6
+
+
+# Check the results against precomputed results
+
+for prefix in ${output_prefixes}; do
+ ${thisdir}/MoveBySuscFeeds.py ${odir} `basename ${prefix}` \
+ `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` \
+ `imglob -extension ${prefix}` \
+ `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` \
+ `imglob -extension ${prefix}.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} ${max_max_dfield_diff}
+done
diff --git a/eddy/feedsRun.EddyS2VTest b/eddy/feedsRun.EddyS2VTest
new file mode 100755
index 0000000..a511d5d
--- /dev/null
+++ b/eddy/feedsRun.EddyS2VTest
@@ -0,0 +1,81 @@
+#! /bin/sh
+#
+# This script runs eddy on data with intra-volume movement,
+# followed by some tests on the output.
+# It uses simulated data supplied by Mark
+# Graham, UCL, which allows us to have a ground
+# truth. The data is a subset of that used
+# for the s2v paper.
+# The script was updated in May 2021 to test also the openmp
+# version.
+#
+
+set -e
+
+thisdir=$(cd $(dirname $0) && pwd)
+odir=$1
+indir=$2
+
+#
+# Inputs 1--3 are the ones neccessary for feeds to work
+# Additional inputs are optional and intended for testing
+# outside of the feeds context.
+#
+# Input 4 is alternative location of executable
+#
+if [ "$#" -gt 3 ]; then
+ exedir=$4
+ echo "Directory for eddy executables set to ${exedir}"
+else
+ exedir="${FSLDIR}/bin"
+fi
+
+if [ ! -d "$odir" ]; then
+ echo "Output directory ${odir} does not exist"
+ exit 1;
+fi
+if [ ! -d "$indir" ]; then
+ echo "Input directory ${odir} does not exist"
+ exit 1;
+fi
+
+# Prepare arguments to pass to eddy
+eddy_args="--imain=${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=${indir}/EddyS2VTestData/eddyData/testAcqparams " \
+ "--repol --ol_type=slice --ol_nstd=6 --ol_nvox=500 " \
+ "--niter=8 --fwhm=10,6,4,2,0,0,0,0 --nvoxhp=5000 " \
+ "--mporder=16 --s2v_niter=10 --s2v_interp=trilinear " \
+ "--s2v_lambda=1 --very_verbose " \
+ "--slspec=${indir}/EddyS2VTestData/eddyData/testSlspec "
+
+# run eddy
+output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
+
+# Define some constants
+# These are for the comparison of output images divided on b=0, b=700 and b=2000
+max_ima_diff="2.0 2.5 0.6 0.7 0.5 0.6"
+# Translations
+max_trans_diff="0.2 1.0"
+# Rotations
+max_rot_diff="0.2 2.0"
+# Outliers
+max_false_pos=10
+max_false_neg=10
+
+# Check the results against ground truth
+for prefix in ${output_prefixes}; do
+ ${thisdir}/S2VFeeds.py ${odir} `basename ${prefix}` \
+ `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` \
+ ${indir}/EddyS2VTestData/eddyData/testBvals \
+ `imglob -extension ${prefix}` \
+ `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` \
+ ${prefix}.eddy_movement_over_time \
+ ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time \
+ ${prefix}.eddy_outlier_map \
+ ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt \
+ ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}
+done
diff --git a/eddy/feedsRun.EddyTest b/eddy/feedsRun.EddyTest
new file mode 100755
index 0000000..c50ac5e
--- /dev/null
+++ b/eddy/feedsRun.EddyTest
@@ -0,0 +1,71 @@
+#!/bin/sh
+#
+# This script runs eddy followed by some
+# tests on the output.
+# It uses simulated data supplied by Mark
+# Graham, UCL, which allows us to have a ground
+# truth. The data is a subset of that used
+# for the outlier paper.
+#
+
+set -e
+
+thisdir=$(cd $(dirname $0) && pwd)
+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
+
+if [ ! -d "$odir" ]; then
+ echo "Output directory ${odir} does not exist"
+ exit 1;
+fi
+if [ ! -d "$indir" ]; then
+ echo "Input directory ${indir} does not exist"
+ exit 1;
+fi
+
+# Prepare arguments to pass to eddy
+eddy_args="--imain=${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=${indir}/EddyTestData/eddyData/testAcqparams " \
+ "--repol --fwhm=10,0,0,0,0 --dfields -v"
+
+# run eddy
+output_prefixes=$(${thisdir}/runEddy ${exedir} ${odir} ${eddy_args} | tail -n1)
+
+# Define some constants
+max_mean_dfield_diff=0.5
+max_max_dfield_diff=1.0
+max_mean_ima_diff=1.5
+max_max_ima_diff=3.0
+allowed_false_positives=1
+allowed_false_negatives=1
+
+# Check the results against ground truth
+for prefix in ${output_prefixes}; do
+ ${thisdir}/EddyFeeds.py ${odir} `basename ${prefix}` \
+ `imglob -extension ${indir}/EddyTestData/eddyData/testMask` \
+ `imglob -extension ${prefix}` \
+ `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` \
+ ${prefix}.eddy_displacement_fields \
+ ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField \
+ ${prefix}.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}
+done
--
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