110 lines (93 with data), 3.7 kB

/*
 * Transform landmarks using estimated transformation
 *
 * EXAMPLE:
 * >> ~/Applications/Fiji.app/ImageJ-linux64 --java-home /usr/lib/jvm/java-8-openjdk-amd64 \
        --headless apply-bunwarpj-transform-to-landmarks.bsh \
        deformed-bridge.png bridge.png \
        moving-landmarks.pts warped-landmarks.pts bridge_inverse_transf.txt \
        deformed-bridge_direct_transf.txt warped-image.tif
 *
 * Copyright (C) 2019 Ignacio Arganda-Carreras <ignacio.arganda@ehu.eus>
 */

import ij.ImagePlus;
import bunwarpj.MiscTools;
import bunwarpj.trakem2.transform.CubicBSplineTransform;
import bunwarpj.bUnwarpJ_;
import ij.gui.PointRoi;
import ij.IJ;

if( bsh.args.length < 7 )
{
	IJ.log( "apply-bunwarpj-transform-to-landmarks.bsh" );
	IJ.log( "USAGE: apply-bunwarpj-transform-to-landmarks.bsh movingImage fixedImage movingLandmarks outputLandmarks inverseTransFile" );
	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( "       'outputLandmarks' path to output landmarks file to be created (txt/TXT)" );
	IJ.log( "       'inverseTransFile' path to bUnwarpJ transform file to apply to landmarks" );
	IJ.log( "       'directTransFile' path to bUnwarpJ transform file to apply to moving image" );
	IJ.log( "       'outputImage' 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 ] );
outputLandmarks = new File( bsh.args[ 3 ] );
inverseTransFile = new File( bsh.args[ 4 ] );
directTransFile = new File( bsh.args[ 5 ] );
outputImage = new File( bsh.args[ 6 ] );


// read number of intervals
intervals = MiscTools.numberOfIntervalsOfTransformation( inverseTransFile.getAbsolutePath() );
// x B-spline coefficients
cx = new double[ intervals + 3][ intervals + 3 ];
// y B-spline coefficients
cy = new double[ intervals + 3][ intervals + 3 ];
// read coefficients from file
MiscTools.loadTransformation( inverseTransFile.getAbsolutePath(), cx, cy );

// Convert to format understandable by RVSS
ct = new CubicBSplineTransform( intervals, cx, cy, movingImage.getWidth(), movingImage.getHeight() );

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();
}

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

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

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

}

warpedMoving = movingImage.duplicate();
bUnwarpJ_.applyTransformToSource( directTransFile.getAbsolutePath(), fixedImage, warpedMoving );
IJ.save( warpedMoving, outputImage.getAbsolutePath() );