Properly compute SNR and contrast with NaNs.

Author: tinevez

src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAndSNRAnalyzer.java

@@ -108,19 +108,31 @@ public final void process( final Spot spot )
 			final SpotRoi outterRoi = roi.copy();
 			outterRoi.scale( alpha );
 			final IterableInterval< T > neighborhood = SpotUtil.iterable( outterRoi, spot, img );
-			double outterSum = 0.;
+			double totalSum = 0.;
+			int nTotal = 0; // Total number of non-NaN pixels
+
+			// Iterate over the big ROI.
 			for ( final T t : neighborhood )
 			{
 				final double val = t.getRealDouble();
 				if ( Double.isNaN( val ) )
 					continue;
-				outterSum += val;
+				nTotal++;
+				totalSum += val;
 			}
-
+			
+			// Sum intensity inside (over non-NaN pixels).
 			final String sumFeature = makeFeatureKey( TOTAL_INTENSITY, channel );
-			final double innterSum = spot.getFeature( sumFeature );
-			outterSum -= innterSum;
-			meanOut = outterSum / ( outterRoi.area() - roi.area() );
+			final double innerSum = spot.getFeature( sumFeature );
+
+			// Compute number of non-NaN pixels in the inner roi.
+			final int nInner = ( int ) ( innerSum / meanIn );
+
+			// Total number of non-NaN pixels in the outer roi.
+			final int nOut = nTotal - nInner;
+
+			final double outterSum = totalSum - innerSum;
+			meanOut = outterSum / nOut;
 		}
 		else
 		{
@@ -136,7 +148,7 @@ public final void process( final Spot spot )
 			}
 
 			final double radius2 = radius * radius;
-			int nOut = 0; // inner number of pixels
+			int nOut = 0; // Outer number of non-NaN pixels.
 			double sumOut = 0;
 
 			// Compute mean in the outer ring
@@ -147,10 +159,10 @@ public final void process( final Spot spot )
 				final double dist2 = cursor.getDistanceSquared();
 				if ( dist2 > radius2 )
 				{
-					nOut++;
 					final double val = cursor.get().getRealDouble();
 					if ( Double.isNaN( val ) )
 						continue;
+					nOut++;
 					sumOut += val;
 				}
 			}