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#!/bin/sh
# TODO:
# - IVE: flip XZ
# - IVE: project
# - python: calc. Z offset per-wavelength
# - python: apply Z offsets -> new file, ~same size as 1st
# - IVE: find mid-section (or octave?)
# note on midsection: can be done by dividing max-intensity projection by the entire stack, then summing and looking for the PEAK intensity. Why not min intensity? Since the dark rim around the mid-section results in a bright rim when it's the denominator, and the sum of that is high. Try with multiple datasets before relying on it...
# - THEN the current program applies - outputs a new file for each nucleus.
# - on each new file (octave):
# - - re-calc perimeter with spacing=1
# - - calculate EDM for binary image
# - - sort EDM into unique bins
# - - get avg. intensity within each bin for each channel.
datafilename=$1;
polyfilename="$datafilename.pol"
#Z=$2;
BORDER=10
Z=`/opt/bin/find-midsection.sh $1 | tail -n 1`;
echo $Z;
THR=`echo $Z|cut -d " " -f 2`;
#THR=$2;
Z=`echo $Z|cut -d " " -f 1`;
Threshold $datafilename $datafilename.thr -z1=$Z -w1=0 -not_below=$THR -result=mask;
2DObjFinder $datafilename.thr -poly=$polyfilename -border=$BORDER -spacing=4 \
-minpts=300 -exclude_edge -outer_only
perl /opt/bin/copyObjsFromPerims.pl $datafilename $polyfilename $BORDER;