afnipal2colorbar

#!/bin/bash

#read in color table from pal.pal file

palFile=
width=30
height=600
units=px
dpi=240
flip=0
outFile=cbar.pdf

while [ -n "$1" ]; do
    case $1 in
	-pal_file)             palFile="$2";            shift 2;;  # name of AFNI palette file
        -width)                width="$2";              shift 2;;  # width of output
	-height)               height="$2";             shift 2;;  # height of output
	-out_file)             outFile="$2";            shift 2;;  # name of output file (pdf or png tested at the moment)
	-units)                units="$2";              shift 2;;  # units of measurement for output file (currently px or in)
	-dpi)                  dpi="$2";                shift 2;;  # pixel density of output
	*) echo -e "\n[Unrecognized option '$1']\n";
	   exit 1;;
    esac
done

[[ -z "$palFile" || ! -r "$palFile" ]] && echo "Cannot find -pal_file: $palFile" && exit 1

if [[ $units == in ]]; then
    width=$(echo "scale=0; $width*$dpi" | bc )
    height=$(echo "scale=0; $height*$dpi" | bc )
fi

#read hex colors from AFNI pal file. Skip first line, which is header
hexcolors=
while IFS='' read -r line || [[ -n "$line" ]]; do
    hexcolors="${hexcolors} xc:$line"
done < <(tail -n +2 "$palFile")

#echo $hexcolors

#imagemagick command to create smooth gradient of any size
set -x
convert -size ${width}x${height} gradient: -rotate 180 -interpolate Bicubic \
	\( +size ${hexcolors} +append \) -clut -density $dpi -units PixelsPerInch "$outFile"