117 lines (96 with data), 4.0 kB

/*
 * Transform landmarks using estimated transformation
 *
 * EXAMPLE:
 * >> ~/Applications/Fiji.app/ImageJ-linux64 --java-home /usr/lib/jvm/java-8-openjdk-amd64 \
        --headless apply-RVSS-transform.bsh deformed-bridge.png bridge.png \
        moving-landmarks.txt deformed-landmarks2.txt transf/deformed-bridge.xml corrected-bridge.png
 *
 * Copyright (C) 2019 Ignacio Arganda-Carreras <ignacio.arganda@ehu.eus>
 */

import ij.ImagePlus;
import ij.gui.PointRoi;
import ij.IJ;
import ij.plugin.Duplicator;
import register_virtual_stack.Transform_Virtual_Stack_MT;
import mpicbg.trakem2.transform.TransformMesh;
import mpicbg.trakem2.transform.TransformMeshMapping;

if( bsh.args.length < 6 )
{
	IJ.log( "apply-RVSS-transform-to-landmarks.bsh" );
	IJ.log( "USAGE: apply-RVSS-transform-to-landmarks.bsh movingImage fixedImage movingLandmarks deformedLandmarks landmarkTransFile deformedImagePath" );
	IJ.log( "       'movingImage' path to moving image" );
	IJ.log( "       'fixedImage' path to fixed image" );
	IJ.log( "       'movingLandmarks' path to moving landmarks file (txt/TXT)" );
	IJ.log( "       'deformedLandmarks' path to output landmarks file to be created (txt/TXT)" );
	IJ.log( "       'landmarkTransFile' path to RVSS transform file to apply to landmarks (.xml)" );
	IJ.log( "       'deformedImagePath' path to output image file to be created (deformed moving image)" );
	return;
}

movingImage = new ImagePlus( bsh.args[ 0 ] );
fixedImage = new ImagePlus( bsh.args[ 1 ] );
movingLandmarks = new File( bsh.args[ 2 ] );
deformedLandmarks = new File( bsh.args[ 3 ] );
landmarkTransFile = new File( bsh.args[ 4 ] );
deformedImagePath = new File( bsh.args[ 5 ] );

br = new BufferedReader(new FileReader( movingLandmarks.getAbsolutePath() ));

pointList = new ArrayList();

try {
    sb = new StringBuilder();
    line = br.readLine(); // skip tag "points"
    line = br.readLine(); // skip number of points
    line = br.readLine();

    while (line != null) {
        //IJ.log( line );
        fi = new Scanner( line );
        point = new double[2];
		point[0] = fi.nextDouble();
		point[1] = fi.nextDouble();
		pointList.add( point );
        line = br.readLine();
    }

} finally {
    br.close();
}

// Read coordinate transform from file
ct = Transform_Virtual_Stack_MT.readCoordinateTransform( landmarkTransFile.getAbsolutePath() );

// Apply transform to points
deformedPointList = new ArrayList();
for( point : pointList )
{
	newPoint = ct.apply( point );
	deformedPointList.add( newPoint );
	IJ.log( "Moving landmark (" + point[0] + ", " + point[1] + ") => Fixed point (" + newPoint[0] + ", " + newPoint[1] +")"  );
}

try {
	writer = new BufferedWriter(	new OutputStreamWriter(
              new FileOutputStream( deformedLandmarks.getAbsolutePath() ), "utf-8") );

	writer.write("point\n");
	writer.write("" + deformedPointList.size() + "\n");
	for( point : deformedPointList )
	{
   		writer.write("" + point[0] + " " + point[1] + "\n");
	}
	writer.close();
}
catch (IOException ex) {
    IJ.log( ex.printStackTrace());
} finally {

}

// Apply transform to image
mesh = new TransformMesh( ct, 32, movingImage.getWidth(), movingImage.getHeight() );
mapping = new TransformMeshMapping( mesh );

// bounding box
bb = mesh.getBoundingBox();
//IJ.log( "bb.x = " + bb.x + ", bb.y = " + bb.y + ", bb.width = " + bb.width + ", bb.height = " + bb.height );

movingImage.getProcessor().setValue(0);
ip = mapping.createMappedImageInterpolated( movingImage.getProcessor() );

// crop corresponding area based on fixed image
output = new ImagePlus( "output", ip );
output.setRoi( -bb.x, -bb.y, fixedImage.getWidth(), fixedImage.getHeight() );
dup = new Duplicator();

output = dup.run( output, 1, output.getNChannels(), 1 ,1, 1, 1 );

// adjust canvas size just in case the ROI was not long enough
IJ.run(output, "Canvas Size...", "width="+fixedImage.getWidth()+" height="+fixedImage.getHeight()+" position=Center zero");

// Save transformed file
IJ.save( output, deformedImagePath.getAbsolutePath() );