Add 1D specializations of Point and PointMatch for intensity matching

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/solvers/intensity/IntensityMatcher.java

@@ -3,7 +3,6 @@
 import ij.process.ColorProcessor;
 import ij.process.FloatProcessor;
 import mpicbg.models.Affine1D;
-import mpicbg.models.Point;
 import mpicbg.models.PointMatch;
 import mpicbg.models.Tile;
 import net.imglib2.util.Pair;
@@ -93,7 +92,7 @@ public void match(final TileSpec p1, final TileSpec p2, final HashMap<String, Ar
 			if (matchCanContribute) {
 				final double p = pixels1.getf(i);
 				final double q = pixels2.getf(i);
-				final PointMatch pq = new PointMatch(new Point(new double[]{p}), new Point(new double[]{q}), weight1 * weight2);
+				final PointMatch pq = new PointMatch1D(new Point1D(p), new Point1D(q), weight1 * weight2);
 
 				/* first sub-tile label is 1 */
 				final List<PointMatch> matches = get(matrix, label1 - 1, label2 - 1, nCoefficientTiles);
@@ -176,9 +175,9 @@ private static List<PointMatch> compressByBinning(final List<PointMatch> candida
 		for (final Map.Entry<Pair<Integer, Integer>, Double> entry : pairToWeights.entrySet()) {
 			final Pair<Integer, Integer> pair = entry.getKey();
 			final double weight = entry.getValue();
-			final Point p1 = new Point(new double[]{ (double) pair.getA() / nBins });
-			final Point p2 = new Point(new double[]{ (double) pair.getB() / nBins });
-			compressedCandidates.add(new PointMatch(p1, p2, weight));
+			final Point1D p1 = new Point1D((double) pair.getA() / nBins);
+			final Point1D p2 = new Point1D((double) pair.getB() / nBins);
+			compressedCandidates.add(new PointMatch1D(p1, p2, weight));
 		}
 
 		return compressedCandidates;

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/solvers/intensity/Point1D.java

@@ -0,0 +1,24 @@
+package org.janelia.render.client.newsolver.solvers.intensity;
+
+import mpicbg.models.CoordinateTransform;
+import mpicbg.models.Point;
+
+/**
+ * A 1D point. This is used in the intensity matching algorithm and adds an optimized method for applying a
+ * transformation a 1D point. The method doesn't overwrite {@link Point#apply(CoordinateTransform)} since this method
+ * is marked as final in the superclass.
+ */
+public class Point1D extends Point {
+	public Point1D(final double l, final double w) {
+		super(new double[] { l }, new double[] { w });
+	}
+
+	public Point1D(final double l) {
+		this(l, l);
+	}
+
+	public void applyFast(final CoordinateTransform t) {
+		w[0] = l[0];
+		t.applyInPlace(w);
+	}
+}

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/solvers/intensity/PointMatch1D.java

@@ -0,0 +1,31 @@
+package org.janelia.render.client.newsolver.solvers.intensity;
+
+import mpicbg.models.CoordinateTransform;
+import mpicbg.models.PointMatch;
+
+/**
+ * A match of two 1D points. This is used in the intensity matching algorithm and adds an optimized method for computing
+ * the distance of two 1D points.
+ */
+public class PointMatch1D extends PointMatch {
+	public PointMatch1D(final Point1D p1, final Point1D p2) {
+		super(p1, p2);
+	}
+
+	public PointMatch1D(final Point1D p1, final Point1D p2, final double weight) {
+		super(p1, p2, weight);
+	}
+
+	@Override
+	public void apply(final CoordinateTransform t) {
+		final Point1D p1 = (Point1D) this.p1;
+		p1.applyFast(t);
+	}
+
+	@Override
+	public double getDistance(){
+		final Point1D p1 = (Point1D) this.p1;
+		final Point1D p2 = (Point1D) this.p2;
+		return Math.abs(p1.getL()[0] - p2.getL()[0]);
+	}
+}