ImageJ / Fiji: Parses a string representing an affine transormation, applies it to an image, and displays it.

parse_and_transform.groovy

#@Dataset(label="Image to transform") img
#@String(label="affine transform string") affineString
#@UIService ui

import net.imglib2.realtransform.*;
import net.imglib2.view.*;
import net.imglib2.interpolation.*;
import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory;

nd = 3
if( affineString.startsWith( "[3,3]" )){
	println( "2" )
	nd = 2
} else if( affineString.startsWith( "[4,4]" )){ 
	println("3")
}

paramString = affineString.replace( "[3,3](AffineTransform", "" ).replaceAll( "\\) .*", "" ).replaceAll( "[\\]\\[\\s]", "" )
paramDouble = []
for ( p in paramString.split(",") ) {
	paramDouble.add( Double.parseDouble( p ));
}

transform = null;
if( nd == 2 )
	transform = new AffineTransform2D();
else if ( nd == 3 ){
	transform = new AffineTransform3D();
}
transform.set( paramDouble as double[] )
println( transform )
interp = new NLinearInterpolatorFactory()

result = Views.interval( 
	Views.raster(
		RealViews.transform(
				Views.interpolate( Views.extendZero( img ), interp),
				transform )),
	img );

ui.show( "transformed", result )