Merge pull request #84 from JaneliaSciComp/missing-connections

Fix issue with disconnected views

Author: StephanPreibisch

src/main/java/net/preibisch/mvrecon/process/fusion/intensity/IntensityMatcher.java

@@ -308,16 +308,16 @@ public List<CoefficientMatch> match(
             }
             flatCandidates.flip();
 
+            final List<PointMatch> reducedMatches = new ArrayList<>();
             if (flatCandidates.size() > minNumCandidates) {
-                final List<PointMatch> reducedMatches = new ArrayList<>();
                 filter.filter(flatCandidates, reducedMatches);
                 if (reducedMatches.isEmpty()) {
                     LOG.debug("({}, {}) not matched", r1.index, r2.index);
                 } else {
                     LOG.debug("({}, {}) matched: {}", r1.index, r2.index, filter.model());
-                    coefficientMatches.add(new CoefficientMatch(r1.index, r2.index, flatCandidates.size(), reducedMatches));
                 }
             }
+            coefficientMatches.add(new CoefficientMatch(r1.index, r2.index, flatCandidates.size(), reducedMatches));
         }
         return coefficientMatches;
     }

src/main/java/net/preibisch/mvrecon/process/fusion/intensity/IntensitySolver.java

@@ -23,6 +23,7 @@
 package net.preibisch.mvrecon.process.fusion.intensity;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 import java.util.Map;
@@ -37,7 +38,6 @@
 import mpicbg.spim.data.sequence.ViewId;
 import net.imglib2.iterator.IntervalIterator;
 import net.preibisch.mvrecon.process.fusion.intensity.IntensityMatcher.CoefficientMatch;
-import net.preibisch.mvrecon.process.fusion.intensity.mpicbg.FastAffineModel1D;
 import net.preibisch.mvrecon.process.fusion.intensity.mpicbg.Point1D;
 import net.preibisch.mvrecon.process.fusion.intensity.mpicbg.PointMatch1D;
 import org.slf4j.Logger;
@@ -70,12 +70,23 @@ public void connect(
 		if (coefficientMatches.isEmpty())
 			return;
 
+		final boolean disconnected = coefficientMatches.stream()
+				.map(CoefficientMatch::matches)
+				.allMatch(Collection::isEmpty);
+
 		final IntensityTile p1IntensityTile = getIntensityTile(p1);
 		final IntensityTile p2IntensityTile = getIntensityTile(p2);
 		for (final CoefficientMatch coefficientMatch : coefficientMatches) {
 			final Tile<?> st1 = p1IntensityTile.getSubTileAtIndex(coefficientMatch.coeff1());
 			final Tile<?> st2 = p2IntensityTile.getSubTileAtIndex(coefficientMatch.coeff2());
-			st1.connect(st2, coefficientMatch.matches());
+			if (disconnected) {
+				identityConnect(st1, st2, 1E-6);
+			} else {
+				final Collection<PointMatch> matches = coefficientMatch.matches();
+				if (!matches.isEmpty()) {
+					st1.connect(st2, matches);
+				}
+			}
 		}
 		p1IntensityTile.connectTo(p2IntensityTile);
 	}
@@ -177,11 +188,21 @@ private static void equilibrateIntensity(final Tile<?> coefficientTile,
 		coefficientTile.connect(equilibrationTile, Collections.singletonList(eqMatch));
 	}
 
-	private static void identityConnect(final Tile<?> t1, final Tile<?> t2) {
+	// TODO: Here we use (0 -> 0) and (1 -> 1) as point matches that represent
+	//       the identity transform. This made sense in Render (where this code
+	//       is copied from), because image intensities are normalized to [0,1].
+	//       However, we don't normalize intensities in multiview-reconstruciton,
+	//       so probably something else should be used here? Dataset min/max?
+	//       Tile min/max?
+	private static void identityConnect(final Tile<?> t1, final Tile<?> t2, final double weight) {
 		final ArrayList<PointMatch> matches = new ArrayList<>();
-		matches.add(new PointMatch1D(new Point1D(0), new Point1D(0)));
-		matches.add(new PointMatch1D(new Point1D(1), new Point1D(1)));
+		matches.add(new PointMatch1D(new Point1D(0), new Point1D(0), weight));
+		matches.add(new PointMatch1D(new Point1D(1), new Point1D(1), weight));
 		t1.connect(t2, matches);
 	}
 
+	private static void identityConnect(final Tile<?> t1, final Tile<?> t2) {
+		identityConnect(t1, t2, 1.0);
+	}
+
 }