123 lines (105 with data), 5.2 kB

/*
 * Image registration via bUnwarpJ plugin with SIFT features
 *
 * EXAMPLE:
 * >> ~/Applications/Fiji.app/ImageJ-linux64 --java-home /usr/lib/jvm/java-8-openjdk-amd64  \
        --headless apply-SIFT-bUnwarpJ-registration.bsh deformed-bridge.png bridge.png \
        1.6 3 64 1024 8 8 0.92 25 0.05 1 \
        2 0 0 3 0.1 0.1 1.0 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_;
import histogram2.HistogramMatcher;

if( bsh.args.length < 23 )
{
	IJ.log( "bUnwarpJ_align_hist_match_SIFT.bsh" );
	IJ.log( "USAGE: bUnwarpJ_align_hist_match_SIFT.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" );

	// SIFT parameters

 	IJ.log( "       'initialSigma' initial Gaussian blur sigma (SIFT parameter, ex. 1.6)" );
 	IJ.log( "       'steps' steps per scale octave (SIFT parameter, ex. 3)" );
 	IJ.log( "       'minOctaveSize' minimum image size in pixels (SIFT parameter, ex. 64)" );
 	IJ.log( "       'maxOctaveSize' maximum image size in pixels (SIFT parameter, ex. 1024)" );
 	IJ.log( "       'fdSize' feature descriptor size (SIFT parameter, ex. 4)" );
 	IJ.log( "       'fdBins' feature descriptor orientation bins (SIFT parameter, ex. 8)" );
 	IJ.log( "       'rod' closest/next closest ratio (SIFT parameter, ex. 0.92)" );
	IJ.log( "       'maxEpsilon' maximal alignment error in pixels (SIFT parameter, ex. 25)" );
	IJ.log( "       'minInlierRatio' inlier ratio (SIFT parameter, ex. 0.05)" );
	IJ.log( "       'modelIndex' expected transformation (SIFT parameter, 0:Translation, 1:Rigid, 2:Similarity, 3:Affine, 4:Perspective)" );

	// bUnwarpJ parameters

	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 ] );

initialSigma = Float.parseFloat( bsh.args[ 2 ] );
steps = Integer.parseInt( bsh.args[ 3 ] );
minOctaveSize = Integer.parseInt( bsh.args[ 4 ] );
maxOctaveSize = Integer.parseInt( bsh.args[ 5 ] );
fdSize = Integer.parseInt( bsh.args[ 6 ] );
fdBins = Integer.parseInt( bsh.args[ 7 ] );
rod = Float.parseFloat( bsh.args[ 8 ] );
maxEpsilon = Float.parseFloat( bsh.args[ 9 ] );
minInlierRatio = Float.parseFloat( bsh.args[ 10 ] );
modelIndex = Integer.parseInt( bsh.args[ 11 ] );

mode = Integer.parseInt( bsh.args[ 12 ] );
subsampleFactor = Integer.parseInt( bsh.args[ 13 ] );
minScale = Integer.parseInt( bsh.args[ 14 ] );
maxScale = Integer.parseInt( bsh.args[ 15 ] );
divWeight = Double.parseDouble( bsh.args[ 16 ] );
curlWeight = Double.parseDouble( bsh.args[ 17 ] );
landmarkWeight = Double.parseDouble( bsh.args[ 18 ] );
imageWeight = Double.parseDouble( bsh.args[ 19 ] );
consistencyWeight = Double.parseDouble( bsh.args[ 20 ] );
stopThreshold = Double.parseDouble( bsh.args[ 21 ] );
movingTransfFile = new File( bsh.args[ 22 ] );
if( bsh.args.length >= 23 )
	fixedTransfFile = new File( bsh.args[ 23 ] );

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

/* IGNORING HIST. MATCHING
    // histogram matching
    ip1 = movingImage.getProcessor();
    ip2 = fixedImage.getProcessor();

    hist1 = ip1.getHistogram();
    hist2 = ip2.getHistogram();

    matcher = new HistogramMatcher();
    newHist = matcher.matchHistograms(hist1, hist2);

    ip1.applyTable( newHist );
    movingImage.setProcessor( ip1 );
*/

// SIFT
sift = new SIFT_ExtractPointRoi();
sift.exec( fixedImage, movingImage,
			initialSigma, steps,
			minOctaveSize, maxOctaveSize,
			fdSize, fdBins,
			rod, maxEpsilon,
			minInlierRatio, modelIndex );

// 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() );