Add ModelFitter to directly fit mpicbg AffineModels

pom.xml

@@ -146,5 +146,11 @@
 			<groupId>gov.nist.math</groupId>
 			<artifactId>jama</artifactId>
 		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<scope>test</scope>
+		</dependency>
 	</dependencies>
 </project>

src/main/java/ch/fmi/ModelFitter.java

@@ -0,0 +1,167 @@
+
+package ch.fmi;
+
+import java.util.ArrayList;
+import mpicbg.models.Affine2D;
+import mpicbg.models.Affine3D;
+import mpicbg.models.AffineModel2D;
+import mpicbg.models.AffineModel3D;
+import mpicbg.models.IllDefinedDataPointsException;
+import mpicbg.models.Model;
+import mpicbg.models.NotEnoughDataPointsException;
+import mpicbg.models.Point;
+import mpicbg.models.PointMatch;
+import mpicbg.models.RigidModel2D;
+import mpicbg.models.RigidModel3D;
+import mpicbg.models.SimilarityModel2D;
+import mpicbg.models.SimilarityModel3D;
+import mpicbg.models.TranslationModel2D;
+import mpicbg.models.TranslationModel3D;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+@Plugin(type = Command.class, headless = true,
+	menuPath = "FMI>Fit Transformation Model to Paired Point Sets")
+public class ModelFitter implements Command {
+
+	final static protected String TRANSLATION = "Translation";
+	final static protected String RIGID = "Rigid";
+	final static protected String SIMILARITY = "Similarity";
+	final static protected String AFFINE = "Affine";
+	final static protected String DIM2D = "2D";
+	final static protected String DIM3D = "3D";
+
+	@Parameter(label = "Type of Transformation", choices = { TRANSLATION, RIGID,
+		SIMILARITY, AFFINE })
+	private String transformType;
+
+	@Parameter(label = "Dimensionality", choices = { DIM2D, DIM3D })
+	private String dim;
+
+	@Parameter(label = "Set 1 - X Coordinates")
+	private double[] x1;
+
+	@Parameter(label = "Set 1 - Y Coordinates")
+	private double[] y1;
+
+	@Parameter(label = "Set 1 - Z Coordinates", required = false)
+	private double[] z1 = null;
+
+	@Parameter(label = "Set 2 - X Coordinates")
+	private double[] x2;
+
+	@Parameter(label = "Set 2 - Y Coordinates")
+	private double[] y2;
+
+	@Parameter(label = "Set 2 - Z Coordinates", required = false)
+	private double[] z2 = null;
+
+	@Parameter(type = ItemIO.OUTPUT)
+	private double[] affine;
+
+	private Model<?> model;
+
+	@Override
+	public void run() {
+		// Choose model
+		switch (transformType) {
+			case TRANSLATION:
+				model = dim.equals(DIM2D) ? //
+					new TranslationModel2D() : new TranslationModel3D();
+				break;
+			case RIGID:
+				model = dim.equals(DIM2D) ? //
+					new RigidModel2D() : new RigidModel3D();
+				break;
+			case SIMILARITY:
+				model = dim.equals(DIM2D) ? //
+					new SimilarityModel2D() : new SimilarityModel3D();
+				break;
+			case AFFINE:
+				model = dim.equals(DIM2D) ? //
+					new AffineModel2D() : new AffineModel3D();
+				break;
+		}
+
+		// Prepare point correspondences (assuming positional correspondence)
+		assert x1.length == y1.length : "X and Y vectors for first point set need to be equal length";
+		assert x2.length == y2.length : "X and Y vectors for second point set need to be equal length";
+		assert x1.length == x2.length : "Both point sets need to have equal length";
+
+		ArrayList<PointMatch> correspondences = new ArrayList<>();
+		for (int i = 0; i < x1.length; i++) {
+			double[] pos1 = new double[dim.equals(DIM2D) ? 2 : 3];
+			pos1[0] = x1[i];
+			pos1[1] = y1[i];
+			if (dim.equals(DIM3D)) pos1[2] = z1[i];
+			Point p1 = new Point(pos1);
+			double[] pos2 = new double[dim.equals(DIM2D) ? 2 : 3];
+			pos2[0] = x2[i];
+			pos2[1] = y2[i];
+			if (dim.equals(DIM3D)) pos2[2] = z2[i];
+			Point p2 = new Point(pos2);
+			correspondences.add(new PointMatch(p1, p2));
+		}
+
+		// Fit the model
+		try {
+			model.fit(correspondences);
+		}
+		catch (NotEnoughDataPointsException exc) {
+			// TODO Auto-generated catch block
+			exc.printStackTrace();
+		}
+		catch (IllDefinedDataPointsException exc) {
+			// TODO Auto-generated catch block
+			exc.printStackTrace();
+		}
+
+		// Retrieve results
+		affine = new double[12];
+		double[] temp;
+		switch (dim) {
+			case DIM2D:
+				temp = new double[6];
+				((Affine2D<?>) model).toArray(temp);
+				map2DColsTo3DRows(temp, affine);
+				break;
+			case DIM3D:
+				temp = new double[12];
+				((Affine3D<?>) model).toArray(temp);
+				mapColsToRows(temp, affine);
+				break;
+		}
+	}
+
+	private void map2DColsTo3DRows(double[] temp, double[] mat) {
+		mat[0] = temp[0];
+		mat[1] = temp[2];
+		mat[2] = 0; //
+		mat[3] = temp[4];
+		mat[4] = temp[1];
+		mat[5] = temp[3];
+		mat[6] = 0; //
+		mat[7] = temp[5];
+		mat[8] = 0; //
+		mat[9] = 0; //
+		mat[10] = 1; //
+		mat[11] = 0; //
+	}
+
+	private void mapColsToRows(double[] temp, double[] mat) {
+		mat[0] = temp[0];
+		mat[1] = temp[3];
+		mat[2] = temp[6];
+		mat[3] = temp[9];
+		mat[4] = temp[1];
+		mat[5] = temp[4];
+		mat[6] = temp[7];
+		mat[7] = temp[10];
+		mat[8] = temp[2];
+		mat[9] = temp[5];
+		mat[10] = temp[8];
+		mat[11] = temp[11];
+	}
+}

src/test/java/ch/fmi/ModelFitterTest.java

@@ -0,0 +1,148 @@
+
+package ch.fmi;
+
+import static org.junit.Assert.assertArrayEquals;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.concurrent.ExecutionException;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.scijava.Context;
+import org.scijava.command.CommandModule;
+import org.scijava.command.CommandService;
+
+public class ModelFitterTest {
+
+	private Context context;
+
+	@Before
+	public void initialize() {
+		context = new Context();
+	}
+
+	@After
+	public void disposeContext() {
+		if (context != null) {
+			context.dispose();
+			context = null;
+		}
+	}
+
+	@Test
+	public void test3DSimilarityModel() throws InterruptedException,
+		ExecutionException
+	{
+		// Create Point Arrays
+		double[] x1 = { 0, 1, 1, 1 };
+		double[] y1 = { 0, 0, 1, 1 };
+		double[] z1 = { 0, 0, 0, 1 };
+		double[] x2 = { 2, 2, 4, 4 };
+		double[] y2 = { 0, -2, -2, -2 };
+		double[] z2 = { 0, 0, 0, 2 };
+
+		Map<String, Object> inputMap = new HashMap<>();
+		inputMap.put("transformType", ModelFitter.SIMILARITY);
+		inputMap.put("dim", ModelFitter.DIM3D);
+		inputMap.put("x1", x1);
+		inputMap.put("y1", y1);
+		inputMap.put("z1", z1);
+		inputMap.put("x2", x2);
+		inputMap.put("y2", y2);
+		inputMap.put("z2", z2);
+
+		// Fit Model
+		CommandService commandService = context.getService(CommandService.class);
+		CommandModule module = commandService.run(ModelFitter.class, true, inputMap)
+			.get();
+
+		// Compare
+		double[] expected = { //
+			0, 2, 0, 2, //
+			-2, 0, 0, 0, //
+			0, 0, 2, 0 //
+		};
+		double[] result = (double[]) module.getOutput("affine");
+		System.out.println(Arrays.toString(result));
+		assertArrayEquals("Affine matrix", expected, result, 0.01);
+	}
+
+	@Test
+	public void test3DAffineModel() throws InterruptedException,
+		ExecutionException
+	{
+		// Create Point Arrays
+		double[] x1 = { 0, 1, 1, 1 };
+		double[] y1 = { 0, 0, 1, 1 };
+		double[] z1 = { 0, 0, 0, 1 };
+		double[] x2 = { 2, 2, 4, 4 };
+		double[] y2 = { 0, -2, -3, -3 };
+		double[] z2 = { 0, 0, 0, 2 };
+
+		Map<String, Object> inputMap = new HashMap<>();
+		inputMap.put("transformType", ModelFitter.AFFINE);
+		inputMap.put("dim", ModelFitter.DIM3D);
+		inputMap.put("x1", x1);
+		inputMap.put("y1", y1);
+		inputMap.put("z1", z1);
+		inputMap.put("x2", x2);
+		inputMap.put("y2", y2);
+		inputMap.put("z2", z2);
+
+		// Fit Model
+		CommandService commandService = context.getService(CommandService.class);
+		CommandModule module = commandService.run(ModelFitter.class, true, inputMap)
+			.get();
+
+		// Compare
+		double[] expected = { //
+			0, 2, 0, 2, //
+			-2, -1, 0, 0, //
+			0, 0, 2, 0 //
+		};
+		double[] result = (double[]) module.getOutput("affine");
+		System.out.println(Arrays.toString(result));
+		assertArrayEquals("Affine matrix", expected, result, 0.01);
+	}
+
+	@Test
+	public void test2DAffineModel() throws InterruptedException,
+		ExecutionException
+	{
+		// Create Point Arrays
+		double[] x1 = { 0, 1, 1, 0 };
+		double[] y1 = { 0, 0, 1, 1 };
+		double[] x2 = { 2, 2, 4, 4 };
+		double[] y2 = { 0, -2, -3, -1 };
+
+		Map<String, Object> inputMap = new HashMap<>();
+		inputMap.put("transformType", ModelFitter.AFFINE);
+		inputMap.put("dim", ModelFitter.DIM2D);
+		inputMap.put("x1", x1);
+		inputMap.put("y1", y1);
+		inputMap.put("x2", x2);
+		inputMap.put("y2", y2);
+
+		inputMap.put("z1", x1); // dummy input
+		inputMap.put("z2", x1); // dummy input
+
+		// Fit Model
+		CommandService commandService = context.getService(CommandService.class);
+		CommandModule module = commandService.run(ModelFitter.class, true, inputMap)
+			.get();
+
+		// Compare
+		double[] expected = { //
+			0, 2, 0, 2, //
+			-2, -1, 0, 0, //
+			0, 0, 1, 0 //
+		};
+
+		double[] result = (double[]) module.getOutput("affine");
+		System.out.println(Arrays.toString(result));
+
+		assertArrayEquals("Affine matrix", expected, result, 0.01);
+	}
+}