#!/bin/sh

# viena_createpng
#
# Script to create png images for VIENA HTML report.
# Uses FSL routines and has as input intermediates from VIENA calculation.
#
#
#   This code is released to the public domain.
#
#   The VIENA modification of SIENA was implemented at the Department of Radiology of the VU University Medical Center, Amsterdam, The Netherlands
#   Authors: Hugo Vrenken, Ingrid Sluimer, Veronica Popescu, Ronald van Schijndel and Adriaan Versteeg. 
#   Questions or comments can be sent to: H.Vrenken@vumc.nl
# 
#   Neither the VU University Medical Center, the University of Oxford, nor any of
#   their employees imply any warranty of usefulness of this software
#   for any purpose, and do not assume any liability for damages,
#   incidental or otherwise, caused by any use of this document or software.



A=A
B=B

# --- ventricle mask on inputs (halfway space)

# ventricle mask in halfway space A to B
# the range 0.9 3 gives red 
${FSLDIR}/bin/overlay 0 0 -c \
    ${A}_halfwayto_${B} -a \
    ${A}_halfwayto_${B}_ventricle_region_bin 0.9 3 \
    ${A}_halfwayto_${B}_ventricle_region_bin_grot

${FSLDIR}/bin/slicer ${A}_halfwayto_${B}_ventricle_region_bin_grot -a \
    ${A}_halfwayto_${B}_ventricle_region_bin.png

${FSLDIR}/bin/imrm ${A}_halfwayto_${B}_ventricle_region_bin_grot

# ventricle mask in halfway space B to A
# the range 0.9 3 gives red 
${FSLDIR}/bin/overlay 0 0 -c \
    ${B}_halfwayto_${A} -a \
    ${B}_halfwayto_${A}_ventricle_region_bin 0.9 3 \
    ${B}_halfwayto_${A}_ventricle_region_bin_grot

${FSLDIR}/bin/slicer ${B}_halfwayto_${A}_ventricle_region_bin_grot -a \
    ${B}_halfwayto_${A}_ventricle_region_bin.png

${FSLDIR}/bin/imrm ${B}_halfwayto_${A}_ventricle_region_bin_grot

# --- flow within ventricle mask

${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow_ventricles -mul -1 ${A}_to_${B}_flowneg_ventricles

${FSLDIR}/bin/overlay 0 0 \
    ${A}_halfwayto_${B} -a \
    ${A}_to_${B}_flow_ventricles 0.01 1 \
    ${A}_to_${B}_flowneg_ventricles 0.01 1 \
    ${A}_halfwayto_${B}_render_ventricles

${FSLDIR}/bin/slicer ${A}_halfwayto_${B}_render_ventricles \
    -s 1 \
    -x 0.4 ven_gr${A}_halfwayto_${B}a.png \
    -x 0.5 ven_gr${A}_halfwayto_${B}b.png \
    -x 0.6 ven_gr${A}_halfwayto_${B}c.png \
    -y 0.4 ven_gr${A}_halfwayto_${B}d.png \
    -y 0.5 ven_gr${A}_halfwayto_${B}e.png \
    -y 0.6 ven_gr${A}_halfwayto_${B}f.png \
    -z 0.4 ven_gr${A}_halfwayto_${B}g.png \
    -z 0.5 ven_gr${A}_halfwayto_${B}h.png \
    -z 0.6 ven_gr${A}_halfwayto_${B}i.png

${FSLDIR}/bin/pngappend ven_gr${A}_halfwayto_${B}a.png \
    + ven_gr${A}_halfwayto_${B}b.png \
    + ven_gr${A}_halfwayto_${B}c.png \
    + ven_gr${A}_halfwayto_${B}d.png \
    + ven_gr${A}_halfwayto_${B}e.png \
    + ven_gr${A}_halfwayto_${B}f.png \
    + ven_gr${A}_halfwayto_${B}g.png \
    + ven_gr${A}_halfwayto_${B}h.png \
    + ven_gr${A}_halfwayto_${B}i.png \
    ${A}_halfwayto_${B}_render_ventricles.png

/bin/rm ven_gr${A}_halfwayto_${B}?.???
${FSLDIR}/bin/imrm ${A}_to_${B}_flowneg_ventricles ${A}_halfwayto_${B}_render_ventricles

# --- end

exit 0