An imagej2 example script for running bigwarp and getting at its landmark pairs

bigwarpDemo.groovy

#@ Dataset (label="moving image") mvgImg
#@ Dataset (label="target image") tgtImg
#@ File (label="landmarks file csv", required=false ) landmarksFile

import bdv.util.*;
import bdv.viewer.*;
import net.imagej.*;

import bigwarp.*;

import net.imglib2.*;
import net.imglib2.util.*;
import net.imglib2.type.numeric.*;
import net.imglib2.realtransform.*;


/**
 * Build a bdv source from a imagej2 Dataset
 */
def srcFromDataset( Dataset data )
{
	
	axisScales = new double[ 3 ];
	for (i in (0..2)){
		axisScales[ i ] = mvgImg.axis( i ).calibratedValue( 1.0 );
	}
	
	srcTransform = new AffineTransform3D();
	srcTransform.set( 
			axisScales[0], 0, 0, 0, 
			0, axisScales[1], 0, 0,
			0, 0, axisScales[2], 0 );

	println( srcTransform )
	return new RandomAccessibleIntervalSource( 
		data, (NumericType)Util.getTypeFromInterval( data ), 
		srcTransform, data.getName());
}

// make bigwarp sources from the dataset 
mvgSrcList = [ srcFromDataset( mvgImg )] as Source[];
tgtSrcList = [ srcFromDataset( tgtImg )] as Source[];

// set up bigwarp
bw = new BigWarp( BigWarpInit.createBigWarpData( mvgSrcList, tgtSrcList, null ), "bigwarp", null );

// load landmarks if there are any
if( landmarksFile != null )
	bw.getLandmarkPanel().getTableModel().load( landmarksFile );


// loop through landmarks
landmarkTable = bw.getLandmarkPanel().getTableModel();
for (i in (0..<landmarkTable.getRowCount()))
{
	println( i )
	mvgImagePoint = landmarkTable.getMovingPoint( i )
	tgtImagePoint = landmarkTable.getFixedPoint( i )
	println( mvgImagePoint )
	println( tgtImagePoint ) 
	println( ' ' )
}