Ignore NaNs in images when computing intensity-related features.

Fix #258
trackmate-sc · Jul 6, 2023 · 8b63ac5 · 8b63ac5
1 parent 90544a7
commit 8b63ac5
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Showing 2 changed files with 17 additions and 3 deletions.
diff --git a/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAndSNRAnalyzer.java b/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAndSNRAnalyzer.java
@@ -110,7 +110,12 @@ public final void process( final Spot spot )
 			final IterableInterval< T > neighborhood = SpotUtil.iterable( outterRoi, spot, img );
 			double outterSum = 0.;
 			for ( final T t : neighborhood )
-				outterSum += t.getRealDouble();
+			{
+				final double val = t.getRealDouble();
+				if ( Double.isNaN( val ) )
+					continue;
+				outterSum += val;
+			}
 
 			final String sumFeature = makeFeatureKey( TOTAL_INTENSITY, channel );
 			final double innterSum = spot.getFeature( sumFeature );
@@ -143,7 +148,10 @@ public final void process( final Spot spot )
 				if ( dist2 > radius2 )
 				{
 					nOut++;
-					sumOut += cursor.get().getRealDouble();
+					final double val = cursor.get().getRealDouble();
+					if ( Double.isNaN( val ) )
+						continue;
+					sumOut += val;
 				}
 			}
 			meanOut = sumOut / nOut;
@@ -159,3 +167,4 @@ public final void process( final Spot spot )
 		spot.putFeature( makeFeatureKey( SNR, channel ), snr );
 	}
 }
+
diff --git a/src/main/java/fiji/plugin/trackmate/features/spot/SpotIntensityMultiCAnalyzer.java b/src/main/java/fiji/plugin/trackmate/features/spot/SpotIntensityMultiCAnalyzer.java
@@ -58,7 +58,12 @@ public void process( final Spot spot )
 		final DoubleArray intensities = new DoubleArray();
 
 		for ( final T pixel : neighborhood )
-			intensities.addValue( pixel.getRealDouble() );
+		{
+			final double val = pixel.getRealDouble();
+			if ( Double.isNaN( val ) )
+				continue;
+			intensities.addValue( val );
+		}
 
 		Util.quicksort( intensities.getArray(), 0, intensities.size() - 1 );
 		spot.putFeature( SpotIntensityMultiCAnalyzerFactory.makeFeatureKey( MEAN_INTENSITY, channel ), Double.valueOf( TMUtils.average( intensities ) ) );