make_mesh.sh

#!/usr/bin/env bash

#add parent directory to PYTONPATH
D=$(cd ../ && pwd)
export PYTHONPATH="${PYTHONPATH}:$D"

#default
CUT=false
MASK=false
BOUNDARY=false

USAGE="usage:\n\
	'basename $0' -i <image file> -t <treshhold> [-m <mask-file>] [-c] [-s <size> -a <axis> -d <direction>] [-b] [-x]\n\
	-i: Image file name to create mesh from. Nifti format required.
	-t: Treshhold for marching cube algorithm
	-m: Optional mask file to be provided. Will be resampled to resolution of image file. If not specified, mask is created out of Image.
	-c: invokes additional function that trims brain image prior to mesh creation. Identifies image boundaries (non-zero entries) and Need to specify
	-s: size of cut in voxel
	-a: axis along which to cut (0,1,2)
	-d: {^beginning','end'}.Direction of cut. Trim either from start of axis inwards or from end of axis inwards.
	-b: use the given mask as boundary for cut
	-x: use Blenders mesh triangulation algorithm to decimate resulting mesh and smooth mesh. Requires working installation of Blender.
	-h: displays help message."

#read options
while getopts ':i:t:bcs:a:d:m:hx' flag; do
	case "${flag}" in
		i)
			IMAGE_NAME="$OPTARG"
			;;
		t)
			TRESHHOLD="$OPTARG"
			;;
		b)
			BOUNDARY=true
			;;
		c)
			CUT=true
			;;
		s)
			SIZE="$OPTARG"
			;;
		a)
			AXIS="$OPTARG"
			;;
		d)
			TRIM_STARTING_FROM="$OPTARG"
			;;
		m)
			MASK=true
			MASK_FILE="$OPTARG"
			;;
		x)
			DECIMATE=true
			;;
		h)
			echo -e "$USAGE"
			exit 0
			;;
	esac
done


if $MASK; then
	RESOLUTION=$(fslinfo $IMAGE_NAME | grep pixdim1)
	RESOLUTION=($(echo $RESOLUTION | tr " " "\n"))
	RESOLUTION=${RESOLUTION[1]}
	CM=x
	RESOLUTION=$RESOLUTION$CM$RESOLUTION$CM$RESOLUTION
	NAME=($(echo $MASK_FILE | tr "." "\n"))
	PREFIX=${NAME[0]}
	SUFFIX=_resampled.nii
	MASK_NAME=$PREFIX$SUFFIX
	echo ResampleImage 3 $MASK_FILE $MASK_NAME $RESOLUTION size=1 spacing=0 1
	ResampleImage 3 $MASK_FILE $MASK_NAME $RESOLUTION size=1 spacing=0 1
fi
if [ "$MASK" == "false" ]; then
	NAME=($(echo $IMAGE_NAME | tr "." "\n"))
	PREFIX=${NAME[0]}
	SUFFIX=_mask.nii
	MASK_NAME=$PREFIX$SUFFIX
	fslmaths $IMAGE_NAME -thr 10 -bin $MASK_NAME
fi

echo mask created

NAME_M=($(echo $MASK_NAME | tr "." "\n"))
PREFIX_M=${NAME_M[0]}
SUFFIX_M=_smoothed.nii
SMOOTHED_MASK=$PREFIX_M$SUFFIX_M


#smooth one mask 
SmoothImage 3 $MASK_NAME 6 $SMOOTHED_MASK

#make mesh using marching cube. 
echo mask smoothed

if $CUT; then
	NAME_C=($(echo $IMAGE_NAME | tr "." "\n"))
	PREFIX_C=${NAME_C[0]}
	SUFFIX_C="_cut.nii"
	OUTPUTFILE=$PREFIX_C$SUFFIX_C
	if $BOUNDARY; then
		python -c "import make_mesh; make_mesh.cut_img_mas(\"$IMAGE_NAME\",\"$OUTPUTFILE\",$SIZE,$AXIS,\"$TRIM_STARTING_FROM\",\"$MASK_NAME\")"
		IMAGE_NAME=$OUTPUTFILE
	else
		python -c "import make_mesh; make_mesh.cut_img_mas(\"$IMAGE_NAME\",\"$OUTPUTFILE\",$SIZE,$AXIS,\"$TRIM_STARTING_FROM\")"
		IMAGE_NAME=$OUTPUTFILE
	fi
	echo Image cut
fi

if [ -f make_mesh.py ]; then
	python make_mesh.py -i $IMAGE_NAME -m $SMOOTHED_MASK -t $TRESHHOLD
else
	python ../make_mesh.py -i $IMAGE_NAME -m $SMOOTHED_MASK -t $TRESHHOLD
fi

echo mesh created


#Decimate and smooth mesh using Blender 
if $DECIMATE; then
	MESH_NAME=$(find . -name '*.obj')
	NAMES=($(echo $MESH_NAME | tr "\n" "\n"))

	if [ -f decimate_mesh_blender.py ]; then
		for NAME in "${NAMES[@]}"
		do
			blender -b -P decimate_mesh_blender.py -- -f $NAME -r 0.4 -i 2 -n 4 -l 0.5
			rm $NAME
		done
	else
		for NAME in "${NAMES[@]}"
		do
			blender -b -P ../decimate_mesh_blender.py -- -f $NAME -r 0.4 -i 2 -n 4 -l 0.5
			rm $NAME
		done
	fi

	echo mesh processed
fi

#Clean UP
rm $SMOOTHED_MASK
rm $OUTPUTFILE
rm $MASK_NAME