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#!/bin/bash
VERSION="0.0.0 test"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
PROGRAMS[0]=ExtractSliceFromImage
PROGRAMS[1]=PrintHeader
PROGRAMS[2]=TileImages
PROGRAMS[3]=DenoiseImage
PROGRAMS[4]=ImageMath
PROGRAMS[5]=N4BiasFieldCorrection
for (( i = 0; i < ${#PROGRAMS[@]}; i++ ))
do
if ! command -v "${PROGRAMS[$i]}" &> /dev/null
then
echo "The ${PROGRAMS[$i]} program can't be found. Please (re)define \$PATH in your environment."
exit
fi
done
function Usage {
cat <<USAGE
Usage:
`basename $0` outputImage operation whichDirection inputImage [optional parameters]
Operations:
* ExtractAllSlices:
* Convolve (ImageMath):
* DenoiseImage:
* N4BiasFieldCorrection:
* RescaleImage (ImageMath):
* TruncateImageIntensity (ImageMath):
Example:
`basename $0` output.nii.gz DenoiseImage 2 input.nii.gz
--------------------------------------------------------------------------------------
ANTs was created by:
--------------------------------------------------------------------------------------
Brian B. Avants, Nick Tustison and Gang Song
Penn Image Computing And Science Laboratory
University of Pennsylvania
script by Nick Tustison
--------------------------------------------------------------------------------------
Get the latest ANTs version at:
--------------------------------------------------------------------------------------
https://github.com/stnava/ANTs/
--------------------------------------------------------------------------------------
Read the ANTS documentation at:
--------------------------------------------------------------------------------------
http://stnava.github.io/ANTs/
USAGE
exit 1
}
control_c()
# run if user hits control-c
{
echo -en "\n*** User pressed CTRL + C ***\n"
cleanup
exit $?
echo -en "\n*** Script cancelled by user ***\n"
}
# Provide output for Help
if [[ "$1" == "-h" || $# -eq 0 ]];
then
Usage >&2
fi
if [ $# -lt 4 ];
then
echo "Illegal number of parameters ($#)"
Usage >&2
fi
OUTPUT_IMAGE=$1
OPERATION=$2
WHICH_DIRECTION=$3
INPUT_IMAGE=$4
PARAMETERS[0]=$5
PARAMETERS[1]=$6
PARAMETERS[2]=$7
PARAMETERS[3]=$8
PARAMETERS[4]=$9
PARAMETERS[5]=$10
PARAMETERS[6]=$11
SIZE_STRING=$( PrintHeader $INPUT_IMAGE 2 )
SIZE=( ${SIZE_STRING//x/ } )
if [[ ${#SIZE[@]} -ne 3 ]];
then
echo "Error: The input image, $INPUT_IMAGE, is not 3-D."
exit
fi
if [[ ${WHICH_DIRECTION} -gt 2 || ${WHICH_DIRECTION} -lt 0 ]];
then
echo "Error: Direction must be an integer in [0,2 ]"
exit
fi
NUMBER_OF_SLICES=${SIZE[$WHICH_DIRECTION]}
TMP_OUTPUT_DIR=$( mktemp -d )
TMP_OUTPUT_FILE=${TMP_OUTPUT_DIR}/tmp${RANDOM}.nii.gz
ALL_OUTPUT_SLICES=()
for (( i = 0; i < $NUMBER_OF_SLICES; i++ ))
do
echo "$OPERATION (direction $WHICH_DIRECTION, slice $i of $NUMBER_OF_SLICES)"
OUTPUT_DIR=`dirname $OUTPUT_IMAGE`
OUTPUT_SLICE=`basename $OUTPUT_IMAGE`
OUTPUT_SLICE=${OUTPUT_SLICE/\.mha/}
OUTPUT_SLICE=${OUTPUT_SLICE/\.nii\.gz/}
OUTPUT_SLICE=${OUTPUT_SLICE/\.nii/}
OUTPUT_SLICE=${OUTPUT_SLICE/\.nrrd/}
OUTPUT_SLICE="${TMP_OUTPUT_DIR}/${OUTPUT_SLICE}Slice${i}.nii.gz"
ExtractSliceFromImage 3 $INPUT_IMAGE $OUTPUT_SLICE $WHICH_DIRECTION $i
ALL_OUTPUT_SLICES[$i]=$OUTPUT_SLICE
case "$OPERATION" in
"ExtractAllSlices")
mv ${OUTPUT_SLICE} ${OUTPUT_DIR}
;;
"Convolve")
ImageMath 2 $OUTPUT_SLICE Convolve $OUTPUT_SLICE ${PARAMETERS[0]} ${PARAMETERS[1]}
;;
"DenoiseImage")
DenoiseImage -d 2 -i $OUTPUT_SLICE -o $OUTPUT_SLICE -v 0
;;
"N4BiasFieldCorrection")
N4BiasFieldCorrection -d 2 -i $OUTPUT_SLICE -o $OUTPUT_SLICE -v 0 -s 2
;;
"RescaleImage")
ImageMath 2 $OUTPUT_SLICE RescaleImage $OUTPUT_SLICE ${PARAMETERS[0]} ${PARAMETERS[1]}
;;
"TruncateImageIntensity")
ImageMath 2 $OUTPUT_SLICE TruncateImageIntensity $OUTPUT_SLICE ${PARAMETERS[0]} ${PARAMETERS[1]} ${PARAMETERS[2]} ${PARAMETERS[3]}
;;
*)
echo "The operation '$OPERATION' is not an option. See usage: '$0 -h 1'"
exit
;;
esac
done
PERMUTATION_ORDER[0]='2 0 1'
PERMUTATION_ORDER[1]='0 2 1'
PERMUTATION_ORDER[2]='0 1 2'
if [[ $OPERATION != "ExtractAllSlices" ]];
then
TileImages 3 $TMP_OUTPUT_FILE 1x1x0 ${ALL_OUTPUT_SLICES[@]}
PermuteFlipImageOrientationAxes 3 $TMP_OUTPUT_FILE $TMP_OUTPUT_FILE ${PERMUTATION_ORDER[$WHICH_DIRECTION]} 0 0 0 0
CopyImageHeaderInformation $INPUT_IMAGE $TMP_OUTPUT_FILE $OUTPUT_IMAGE 1 1 1
fi
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