canonical_test.sh

#!/bin/bash

#on MacOS use -l for maximum memory details
#/usr/bin/time -l  niimath test4D -add 0 tst

#exe is executable, e.g. fslmaths or niimath
# we assume it is in the users path
# however, this could be set explicitly, e.g.
#  exe="/Users/cr/fslmaths" canonical_test.sh
exe=${exe:-niimath}
#exe=${exe:-fslmaths}

#tstexe is executable with "compare" function, e.g. niimath
#n.b. fslmaths does not have this function
# we assume it is in the users path
# however, this could be set explicitly
tstexe=${tstexe:-niimath}

#basedir is folder with "In" subfolder.
# we assume it is the same same folder as the script
# however, this could be set explicitly, e.g.
#   basedir="/Users/cr/niitest" batch.sh
if [ -z ${basedir:-} ]; then
    basedir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
fi

#### no need to edit subsequent lines

# Fail if anything not planed to go wrong, goes wrong
set -eu

# Test if command exists.
exists() {
    test -x "$(command -v "$1")"
}

# Check executables.
exists $exe ||
    {
        echo >&2 "I require $exe but it's not installed.  Aborting."
        exit 1
    }
exists $tstexe ||
    {
        echo >&2 "I require $tstexe but it's not installed.  Aborting."
        exit 1
    }

#folder paths
indir=${basedir}/In
outdir=${basedir}/New
refdir=${basedir}/Canonical

if [ ! -d "$indir" ]; then
 echo "Error: Unable to find $indir"
 exit 1
fi
if [ ! -d "$refdir" ]; then
 echo "Error: Unable to find $refdir"
 exit 1
fi
if [ ! -d "$outdir" ]; then
 mkdir $outdir
fi
if [ ! -z "$(ls $outdir)" ]; then
 echo "Cleaning output directory: $outdir"
 rm $outdir/*
fi
refout="$refdir/"
newout="$outdir/"

inimg="$indir/trick"
op=demean
echo Testing ${op}
cmd="$exe $inimg -Tmean -mul -1 -add  $inimg ${newout}${op}"
$cmd
tst="$tstexe ${refout}${op} --compare ${newout}${op}"
$tst

ops="thrp uthrp Tperc Xperc Yperc Zperc inm ing add sub mul div rem thr uthr max min"
inimg="$indir/trick"
family="BinaryEven"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op 50 ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="thrP uthrP"
inimg="$indir/trick"
family="BinaryPEven"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op 50 ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="Tperc Xperc Yperc Zperc inm ing add sub mul div rem thr uthr max min"
inimg="$indir/3vols"
family="BinaryOdd"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op 50 ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="Tmedian Xmedian Zmedian"
family="MedianOdd"
inimg="$indir/3vols"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

#ALMOST identical Xar1 Yar1 Zar1
ops="Tmedian Xmedian Zmedian Tar1 Tmean Tstd Tmax Tmaxn Tmin Tar1 Xmean Xstd Xmax Xmaxn Xmin Ymean Ystd Ymax Ymaxn Ymin Zmean Zstd Zmax Zmaxn Zmin"
family="ReduceEven"
inimg="$indir/trick"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

rx="AIL AIR ALI ALS ARI ARS ASL ASR IAL IAR ILA ILP IPL IPR IRA IRP LAI LAS LIA LIP LPI LPS LSA LSP PIL PIR PLI PLS PRI PRS PSL PSR RAI RAS RIA RIP RPI RPS RSA RSP SAL SAR SLA SLP SPL SPR SRA SRP"
## -roi <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> zero outside roi
family="roi"
for op in $rx; do
 inimg="$indir/$op"
 echo Creating ${op}${family}
 cmd="$exe $inimg -roi 5 19 3 22 2 28 0 1 ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

echo Testing Binary Operations: with 2nd image
ops="add sub mul div max min rem"
inimg="$indir/trick"
modimg="$indir/trick3D"
family="Binary2Img"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $inimg -$op $modimg ${newout}${op}${family}"
 $cmd
 # reverse order: not all operations are commutative
 cmd="$exe $modimg -$op $inimg ${newout}${op}${family}Rev"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="exp log sin cos tan asin acos atan sqr sqrt recip abs bin binv fillh fillh26 index nan nanm"
inimg="trick"
family="Unary"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $indir/$inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="dilM dilD dilF ero eroF eroF fmedian subsamp2offc"
inimg="trick3D"
family="Filter"
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $indir/$inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${newout}${op}${family}"
 $tst
done

ops="rank ranknorm"
inimg="$indir/no_ties"
for op in $ops; do
 echo Creating ${op}
 cmd="$exe $inimg -$op ${newout}${op}"
 $cmd
 tst="$tstexe ${refout}${op} --compare ${newout}${op}"
 $tst
done

# band pass temporal filtering
inimg="$indir/rest4D"
echo "Creating bptf (tiny variations expected)"
op=bptfHighPass
thr=0.0001
cmd="$exe $inimg -bptf 25 -1 ${newout}${op}"
$cmd
tst="$tstexe ${refout}${op} --compare ${thr} ${newout}${op}"
$tst
op=bptfLowPass
cmd="$exe $inimg -bptf -1 5 ${newout}${op}"
$cmd
tst="$tstexe ${refout}${op} --compare ${thr} ${newout}${op}"
$tst
op=bptfBandPass
cmd="$exe $inimg -bptf 25 5 ${newout}${op}"
$cmd
tst="$tstexe ${refout}${op} --compare ${thr} ${newout}${op}"
$tst

#Most different voxel 396.58 vs 396.579 (difference 6.10352e-05) location 23x30x1 
ops="edge"
inimg="trick"
family="Unary"
thr=0.0001
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $indir/$inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${thr} ${newout}${op}${family}"
 $tst
done

ops="fmean fmeanu"
inimg="trick3D"
family="Filter"
thr=0.0001
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $indir/$inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${thr} ${newout}${op}${family}"
 $tst
done

#Most different voxel 2.50056 vs 2.93827 (difference 0.437711) location 32x38x21
ops="dilall"
inimg="trick3D"
family="Filter"
thr=0.5
for op in $ops; do
 echo Creating ${op}${family}
 cmd="$exe $indir/$inimg -$op ${newout}${op}${family}"
 $cmd
 tst="$tstexe ${refout}${op}${family} --compare ${thr} ${newout}${op}${family}"
 $tst
done

echo "$exe passed tests"
exit 0