make-import-overlap

#!/bin/bash

# call create-import <file-list> <chunk-size> <min> <max> <type>
#
# create the file list e.g.
#   find `pwd`/raw/ -name "*.tif" | sort > ls-sorted.txt
# chunk-size - the number of layers in one range, overlap is 50%
# min - minimum intensity, mapped to 0 in uint8
# max - maximum intensity, mapped to 255 in uint8
# type - 0: uint8 (gray), 1: uint16 (gray), 2: float32 (gray), 3: uint8 (indexed color), 4s: uint32 (RGB color)
# 

IFS=$'\n'

mod=${2:-100}
min=${3:-11000}
max=${4:-30000}
t=${5:-1}


z=0
zmod=0
zmoda=0

file="$z-$(($mod-1))"
filea="$z-$(($mod/2-1))"
mkdir -p "$file"
mkdir -p "$filea"

for row in `cat "${1}"`
do
	if [ "$zmod" -eq "$mod" ]
	then
		zmod=0
		file="$z-$(($z+$mod-1))"
		mkdir "$file"
	fi
	
	if [ "$zmoda" -eq "$(($mod/2))" ]
	then
		zmoda=$((-$mod/2))
		filea="$z-$(($z+$mod-1))"
		mkdir "$filea"
	fi
	
	echo "$row 0 0 $z - - $min $max $t" >> "${file}/import.txt"
	echo "$row 0 0 $z - - $min $max $t" >> "${filea}/import.txt"
	
	zmod=$(($zmod+1))
	zmoda=$(($zmoda+1))
	z=$(($z+1))
done