conformance.sh

#!/bin/bash

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

#refexe is reference executable, e.g. validated copy of fslmaths
# we assume it is in the users path
# however, this could be set explicitly, e.g.
#  refexe="/Users/cr/fslmaths" batch.sh
refexe=${refexe:-fslmaths}

#newexe is new executable, e.g. we want to make sure if gives the same results as refexe
#  this could also be set explicitly, e.g.
#  refexe="/Users/cr/fslmaths" batch.sh
newexe=${newexe:-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 $refexe ||
    {
        echo >&2 "I require $refexe but it's not installed.  Aborting."
        exit 1
    }
exists $newexe ||
    {
        echo >&2 "I require $newexe but it's not installed.  Aborting."
        exit 1
    }

#folder paths
indir=${basedir}/In
newdir=${basedir}/New
refdir=${basedir}/Ref
if [ ! -d "$indir" ]; then
 echo "Error: Unable to find $indir"
 exit 1
fi
if [ ! -d "$refdir" ]; then
 mkdir $refdir
fi
if [ ! -z "$(ls $refdir)" ]; then
 echo "Cleaning output directory: $refdir"
 rm $refdir/*
fi
if [ ! -d "$newdir" ]; then
 mkdir $newdir
fi
if [ ! -z "$(ls $newdir)" ]; then
 echo "Cleaning output directory: $newdir"
 rm $newdir/*
fi
# Convert images.
refout="$refdir/ref"
newout="$newdir/new"

echo Testing Operation Comibinations: demean
# fslmaths 4D_inputVolume -Tmean -mul -1 -add 4D_inputVolume demeaned_4D_inputVolume
inimg="$indir/trick"
cmd="$refexe $inimg -Tmean -mul -1 -add  $inimg $refout"
echo $cmd
$cmd
cmd="$newexe $inimg -Tmean -mul -1 -add  $inimg $newout"
echo $cmd
$cmd
tst="$newexe $refout --compare $newout"
echo $tst
$tst

echo Testing Binary Operations: with fixed value
#ops="add sub mul div rem thr thrp thrP uthr uthrp uthrP max min"
ops="thrp thrP uthrp uthrP Tperc Xperc Yperc Zperc inm ing add sub mul div rem thr uthr max min"
inimg="$indir/trick"
for op in $ops; do
 cmd="$refexe $inimg -$op 50 $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -$op 50 $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $tst
done

echo Testing Binary Operations: with fixed value with odd number of volumes
#ops="add sub mul div rem thr thrp thrP uthr uthrp uthrP max min"
ops="Tperc Xperc Yperc Zperc inm ing add sub mul div rem thr uthr max min"
 inimg="$indir/3vols"
for op in $ops; do
 cmd="$refexe $inimg -$op 50 $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -$op 50 $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $tst
done


ops="Tmedian Xmedian Zmedian"
echo Median with odd number of volumes
for op in $ops; do
 inimg="$indir/3vols"
 cmd="$refexe $inimg -$op $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -$op $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $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"
echo Testing Dimensionality reduction
for op in $ops; do
 inimg="$indir/trick"
 cmd="$refexe $inimg -$op $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -$op $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $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
for img in $rx; do
 inimg="$indir/$img"
 cmd="$refexe $inimg -roi 5 19 3 22 2 28 0 1 $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -roi 5 19 3 22 2 28 0 1 $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $tst
done

echo Testing Binary Operations: with 2nd image
#ops="add sub mul div rem thr thrp thrP uthr uthrp uthrP max min"
ops="add sub mul div max min rem"
inimg="$indir/trick"
modimg="$indir/trick3D"
for op in $ops; do
 cmd="$refexe $inimg -$op $modimg $refout"
 echo $cmd
 $cmd
 cmd="$newexe $inimg -$op $modimg $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $tst
 # reverse order: not all operations are commutative
 cmd="$refexe $modimg -$op $inimg $refout"
 echo $cmd
 $cmd
 cmd="$newexe $modimg -$op $inimg $newout"
 echo $cmd
 $cmd
 tst="$newexe $refout --compare $newout"
 echo $tst
 $tst
done

echo Testing Basic unary operations
ops="exp log sin cos tan asin acos atan sqr sqrt recip abs bin binv fillh fillh26 index edge nan nanm"
inimg="trick"
for op in $ops; do
 cmd="$refexe $indir/$inimg -$op $refout"
 echo $cmd
 $cmd
 cmd="$newexe $indir/$inimg -$op $newout"
 $cmd
 tst="$newexe $refout --compare $newout"
 $cmd
done

echo Spatial Filtering operations
ops="dilM dilD dilF dilall ero eroF eroF fmedian fmean fmeanu subsamp2offc"
inimg="trick3D"
for op in $ops; do
 cmd="$refexe $indir/$inimg -$op $refout"
 echo $cmd
 $cmd
 cmd="$newexe $indir/$inimg -$op $newout"
 $cmd
 tst="$newexe $refout --compare $newout"
 $cmd
done

echo SUCCESS
exit 0