69 lines (62 with data), 3.1 kB

/*
 * Image registration via bUnwarpJ plugin
 *
 * EXAMPLE:
 * >> ~/Applications/Fiji.app/ImageJ-linux64 --java-home /usr/lib/jvm/java-8-openjdk-amd64 \
        --headless apply_bUnwarpJ.bsh deformed-bridge.png bridge.png \
        2 0 0 3 0.1 0.1 0.0 1.0 10.0 0.01 \
        bridge-direct.txt bridge-inverse.txt
 *
 * Copyright (C) 2019 Ignacio Arganda-Carreras <ignacio.arganda@ehu.eus>
 */

import ij.ImagePlus;
import ij.IJ;
import bunwarpj.bUnwarpJ_;

if( bsh.args.length < 13 )
{
	IJ.log( "bUnwarpJ_align.bsh" );
	IJ.log( "USAGE: apply-bUnwarpJ-registration.bsh movingImage mode subsampleFactor minScale maxScale divWeight curlWeight landmarkWeight imageWeight consistencyWeight stopThreshold" );
	IJ.log( "       'movingImage' path to moving image" );
	IJ.log( "       'fixedImage' path to fixed image" );
	IJ.log( "       'mode' 0-2 (0-Accurate, 1-Fast, 2-Mono)" );
	IJ.log( "       'subsampleFactor' 0-7 (0 = 2^0, 7 = 2^7)" );
	IJ.log( "       'minScale' 0-3 (0-Very Coarse, 1-Coarse, 2-Fine, 3-Very Fine)" );
	IJ.log( "       'maxScale' 0-4 (0-Very Coarse, 1-Coarse, 2-Fine, 3-Very Fine, 4-Super Fine)" );
	IJ.log( "       'divWeight' weight to penalize divergence (Ex. 0.1)" );
	IJ.log( "       'curlWeight' weight to penalize curl (Ex. 0.1)" );
	IJ.log( "       'landmarkWeight' weight to penalize landmark location error (Ex. 1.0)" );
	IJ.log( "       'imageWeight' weight to penalize intensity difference (Ex. 1.0)" );
	IJ.log( "       'consistencyWeight' weight to penalize consistency difference (Ex. 1.0)" );
	IJ.log( "       'stopThreshold' error function stopping threshold value (Ex. 0.01)" );
	IJ.log( "       'movingTransfFile' name of the bUnwarpJ transform file to apply to moving image (output)" );
	IJ.log( "       'fixedTransfFile' name of the bUnwarpJ transform file to apply to fixed image (output [optional])" );
	return;
}

// registration parameters
movingImage = new ImagePlus( bsh.args[ 0 ] );
fixedImage = new ImagePlus( bsh.args[ 1 ] );
mode = Integer.parseInt( bsh.args[ 2 ] );
subsampleFactor = Integer.parseInt( bsh.args[ 3 ] );
minScale = Integer.parseInt( bsh.args[ 4 ] );
maxScale = Integer.parseInt( bsh.args[ 5 ] );
divWeight = Double.parseDouble( bsh.args[ 6 ] );
curlWeight = Double.parseDouble( bsh.args[ 7 ] );
landmarkWeight = Double.parseDouble( bsh.args[ 8 ] );
imageWeight = Double.parseDouble( bsh.args[ 9 ] );
consistencyWeight = Double.parseDouble( bsh.args[ 10 ] );
stopThreshold = Double.parseDouble( bsh.args[ 11 ] );
movingTransfFile = new File( bsh.args[ 12 ] );
if( bsh.args.length >= 13 )
	fixedTransfFile = new File( bsh.args[ 13 ] );

// no masks
maskIpTgt = null;
maskIpSrc = null;

// compute registration without GUI
t = bUnwarpJ_.computeTransformationBatch( fixedImage, movingImage, maskIpTgt, maskIpSrc, mode,
						subsampleFactor, minScale, maxScale,
						divWeight, curlWeight, landmarkWeight,
						imageWeight, consistencyWeight, stopThreshold );

// save transforms
t.saveDirectTransformation( movingTransfFile.getAbsolutePath() );
if( mode < 2 )
	t.saveInverseTransformation( fixedTransfFile.getAbsolutePath() );