Elliposid distance computer

src/main/java/ch/epfl/biop/bdv/command/transform/ComputeEllipse3DTransformedDistanceCommand.java

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+package ch.epfl.biop.bdv.command.transform;
+
+import bdv.util.Elliptical3DTransform;
+import ij.IJ;
+import net.imglib2.util.LinAlgHelpers;
+import org.scijava.Context;
+import org.scijava.ItemIO;
+import org.scijava.command.Command;
+import org.scijava.command.CommandService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
+
+@Plugin(type = Command.class, menuPath = ScijavaBdvDefaults.RootMenu+"Sources>Transform>Compute Ellipsoid Transformed Distance")
+public class ComputeEllipse3DTransformedDistanceCommand implements Command {
+
+    @Parameter
+    public Elliptical3DTransform e3Dt;
+
+    @Parameter ( stepSize = "0.001")
+    public Double radiusA = 1.1;
+
+    @Parameter ( stepSize = "0.001")
+    public Double angle1A = 1.0;
+
+    @Parameter ( stepSize = "0.001")
+    public Double angle2A = 2.4;
+
+    @Parameter ( stepSize = "0.001")
+    public Double radiusB = 1.1;
+
+    @Parameter ( stepSize = "0.001")
+    public Double angle1B = 2.2;
+
+    @Parameter ( stepSize = "0.001")
+    public Double angle2B = 3.8;
+
+    @Parameter ( min = "1" )
+    public int numSteps = 1;
+
+    @Parameter( type = ItemIO.OUTPUT )
+    public Double distance;
+
+    @Override
+    public void run() {
+
+        final double[] pA = new double[ 3 ];
+        pA[ 0 ] = radiusA; pA[ 1 ] = angle1A; pA[ 2 ] = angle2A;
+        final double[] pB = new double[ 3 ];
+        pB[ 0 ] = radiusB; pB[ 1 ] = angle1B; pB[ 2 ] = angle2B;
+
+        distance = computeDistance( pA, pB, numSteps );
+    }
+
+    private double computeDistance( double[] pA, double[] pB, int numSteps )
+    {
+        final double[] vAB = new double[ 3 ];
+        LinAlgHelpers.subtract( pB, pA, vAB );
+
+        final double[] p0 = new double[ 3 ];
+        final double[] p1 = new double[ 3 ];
+        final double[] vStep = new double[ 3 ];
+
+        copy( pA, p0 );
+
+        LinAlgHelpers.scale( vAB, 1.0 / numSteps, vStep );
+
+        double curvedDistance = 0.0;
+        for ( int i = 0; i < numSteps; i++ )
+        {
+            LinAlgHelpers.add( p0, vStep, p1 );
+            curvedDistance += distance( p0, p1 );
+            copy( p1, p0 );
+        }
+
+        return curvedDistance;
+    }
+
+    private void copy( double[] source, double[] target )
+    {
+        for ( int d = 0; d < source.length; d++ )
+            target[ d ] = source[ d ];
+    }
+
+    private double distance( double[] pA, double[] pB )
+    {
+        double[] pAtransformed = new double[ 3 ];
+        double[] pBtransformed = new double[ 3 ];
+        e3Dt.apply( pA, pAtransformed );
+        e3Dt.apply( pB, pBtransformed );
+        return LinAlgHelpers.distance( pAtransformed, pBtransformed );
+    }
+
+    public static void main( String[] args )
+    {
+        Context ctx = (Context ) IJ.runPlugIn("org.scijava.Context", "");
+        CommandService commandService = ctx.service( CommandService.class );
+        commandService.run( ComputeEllipse3DTransformedDistanceCommand.class, true );
+    }
+}

src/test/java/DemoComputeEllipticalDistance.java

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+import bdv.util.Elliptical3DTransform;
+import ch.epfl.biop.bdv.command.transform.ComputeEllipse3DTransformedDistanceCommand;
+import net.imagej.ImageJ;
+import net.imagej.patcher.LegacyInjector;
+
+public class DemoComputeEllipticalDistance
+{
+
+    static {
+        LegacyInjector.preinit();
+    }
+
+    public static void main(String... args) {
+
+        // Initializes static SourceService and Display Service
+        ImageJ ij = new ImageJ();
+        ij.ui().showUI();
+
+        final ComputeEllipse3DTransformedDistanceCommand command = new ComputeEllipse3DTransformedDistanceCommand();
+        Elliptical3DTransform e3Dt = new Elliptical3DTransform();
+        e3Dt.setParameters(
+                "r1", 338.0,
+                "r2", 292.0,
+                "r3", 320.0,
+                "rx", 2.0,
+                "ry", 0.81,
+                "rz", 2.81,
+                "tx", 209.0,
+                "ty", 230.0,
+                "tz", -230.0);
+       command.e3Dt = e3Dt;
+       command.radiusA = 1.1;
+       command.angle1A = 1.0;
+       command.angle2A = 2.4;
+       command.radiusB = 1.1;
+       command.angle1B = 2.2;
+       command.angle2B = 3.8;
+
+       command.numSteps = 1;
+       command.run();
+       System.out.println("Distance, numSteps 1: " + command.distance );
+
+       command.numSteps = 100;
+       command.run();
+       System.out.println("Distance, numSteps 100: " + command.distance );
+    }
+
+}

src/test/java/DemoComputeEllipticalDistanceCommand.java

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+import bdv.util.Elliptical3DTransform;
+import ch.epfl.biop.bdv.command.transform.ComputeEllipse3DTransformedDistanceCommand;
+import ij.IJ;
+import net.imagej.ImageJ;
+import net.imagej.patcher.LegacyInjector;
+import org.scijava.Context;
+import org.scijava.command.CommandService;
+import org.scijava.object.ObjectService;
+
+public class DemoComputeEllipticalDistanceCommand
+{
+
+    static {
+        LegacyInjector.preinit();
+    }
+
+    public static void main(String... args) {
+
+        ImageJ ij = new ImageJ();
+        ij.ui().showUI();
+
+        Elliptical3DTransform e3Dt = new Elliptical3DTransform();
+        e3Dt.setParameters(
+                "r1", 338.0,
+                "r2", 292.0,
+                "r3", 320.0,
+                "rx", 2.0,
+                "ry", 0.81,
+                "rz", 2.81,
+                "tx", 209.0,
+                "ty", 230.0,
+                "tz", -230.0);
+
+
+        Context ctx = (Context ) IJ.runPlugIn("org.scijava.Context", "");
+        ctx.getService( ObjectService.class).addObject( e3Dt );
+        ctx.service( CommandService.class ).run( ComputeEllipse3DTransformedDistanceCommand.class, true );
+    }
+
+}