blockmatching.bsh

import mpicbg.ij.blockmatching.*;
import mpicbg.models.*;
import mpicbg.trakem2.align.*;
import ij.gui.*;

scale = 1.0f;

blockRadius = searchRadius = 50;

minR = 0.1f;
rodR = 1.0f;
maxCurvatureR = 1000.0f;

useLocalSmoothnessFilter = true;
modelStrings = new String[]{ "Translation", "Rigid", "Similarity", "Affine" };
localModelIndex = 1;
localRegionSigma = 65.0f;
maxLocalEpsilon = 12.0f;
maxLocalTrust = 3.0f;

meshResolution = 24;

boolean setup()
{
	gdBlockMatching = new GenericDialog( "Block Matching parameters" );
			
	gdBlockMatching.addMessage( "Block Matching:" );
	gdBlockMatching.addNumericField( "layer_scale :", scale, 2 );
	gdBlockMatching.addNumericField( "search_radius :", searchRadius, 0, 6, "px" );
	gdBlockMatching.addNumericField( "block_radius :", blockRadius, 0, 6, "px" );
	gdBlockMatching.addNumericField( "resolution :", meshResolution, 0 );
	
	gdBlockMatching.addMessage( "Correlation Filters:" );
	gdBlockMatching.addNumericField( "minimal_PMCC_r :", minR, 2 );
	gdBlockMatching.addNumericField( "maximal_curvature_ratio :", maxCurvatureR, 2 );
	gdBlockMatching.addNumericField( "maximal_second_best_r/best_r :", rodR, 2 );
			
	gdBlockMatching.addMessage( "Local Smoothness Filter:" );
	gdBlockMatching.addCheckbox( "use_local_smoothness_filter", useLocalSmoothnessFilter );
	gdBlockMatching.addChoice( "approximate_local_transformation :", modelStrings, modelStrings[ localModelIndex ] );
	gdBlockMatching.addNumericField( "local_region_sigma:", localRegionSigma, 2, 6, "px" );
	gdBlockMatching.addNumericField( "maximal_local_displacement (absolute):", maxLocalEpsilon, 2, 6, "px" );
	gdBlockMatching.addNumericField( "maximal_local_displacement (relative):", maxLocalTrust, 2 );
	
	gdBlockMatching.showDialog();
			
	if ( gdBlockMatching.wasCanceled() )
		return false;
			
	scale = ( float )gdBlockMatching.getNextNumber();
	searchRadius = ( int )gdBlockMatching.getNextNumber();
	blockRadius = ( int )gdBlockMatching.getNextNumber();
	meshResolution = ( int )gdBlockMatching.getNextNumber();
	minR = ( float )gdBlockMatching.getNextNumber();
	maxCurvatureR = ( float )gdBlockMatching.getNextNumber();
	rodR = ( float )gdBlockMatching.getNextNumber();
	useLocalSmoothnessFilter = gdBlockMatching.getNextBoolean();
	localModelIndex = gdBlockMatching.getNextChoiceIndex();
	localRegionSigma = ( float )gdBlockMatching.getNextNumber();
	maxLocalEpsilon = ( float )gdBlockMatching.getNextNumber();
	maxLocalTrust = ( float )gdBlockMatching.getNextNumber();
	
	return true;		
}

FloatProcessor createMask( ImageProcessor source )
{
	mask = new FloatProcessor( source.getWidth(), source.getHeight() );
	maskColor = 0x0000ff00;
	n = source.getWidth() * source.getHeight();
	maskPixels = mask.getPixels();
	for ( int i = 0; i < n; ++i )
	{
		sourcePixel = source.get( i ) & 0x00ffffff;
		if ( sourcePixel == maskColor )
			maskPixels[ i ] = 0;
		else
			maskPixels[ i ] = 1;
	}
	return mask;
}

if ( setup() )
{
	stack = IJ.getImage().getStack();

	mesh = new SpringMesh( meshResolution, stack.getWidth(), stack.getHeight(), 1, 1000, 1 );

	pm12 = new ArrayList();

	v1 = mesh.getVertices();

	ip1 = stack.getProcessor( 1 ).convertToFloat().duplicate();
	ip2 = stack.getProcessor( 2 ).convertToFloat().duplicate();
			
	ip1Mask = createMask( stack.getProcessor( 1 ) );
	ip2Mask = createMask( stack.getProcessor( 2 ) );

	ct = new TranslationModel2D();

	BlockMatching.matchByMaximalPMCC(
			ip1,
			ip2,
			ip1Mask,
			ip2Mask,
			scale,
			ct,
			blockRadius,
			blockRadius,
			searchRadius,
			searchRadius,
			minR,
			rodR,
			maxCurvatureR,
			v1,
			pm12,
			new ErrorStatistic( 1 ) );
	
	IJ.log( pm12.size() + " blockmatch candidates found." );
	
	if ( useLocalSmoothnessFilter )		
	{
		model = mpicbg.trakem2.align.Util.createModel( localModelIndex );
		model.localSmoothnessFilter( pm12, pm12, localRegionSigma, maxLocalEpsilon, maxLocalTrust );
		IJ.log( pm12.size() + " blockmatch candidates passed local smoothness filter." );
	}
		
	pm12Sources = new ArrayList();
	pm12Targets = new ArrayList();

	PointMatch.sourcePoints( pm12, pm12Sources );
	PointMatch.targetPoints( pm12, pm12Targets );

	roi1 = mpicbg.ij.util.Util.pointsToPointRoi( pm12Sources );
	roi2 = mpicbg.ij.util.Util.pointsToPointRoi( pm12Targets );

	imp1 = new ImagePlus( "1", stack.getProcessor( 1 ) );
	imp2 = new ImagePlus( "2", stack.getProcessor( 2 ) );

	imp1.setRoi( roi1 );
	imp2.setRoi( roi2 );
}


imp1.show();
imp2.show();