Merge pull request #224 from fiji/shape-index-feature

'Cell shape index' morphological feature in 2D.

Author: tinevez

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

@@ -69,11 +69,13 @@ public void process( final Spot spot )
 		}
 		final double circularity = 4. * Math.PI * ( area / ( perimeter * perimeter ) );
 		final double solidity = area / convexArea;
-
+		final double shapeIndex = ( area <= 0. ) ? Double.NaN : perimeter / Math.sqrt( area );
+		
 		spot.putFeature( SpotShapeAnalyzerFactory.AREA, area );
 		spot.putFeature( SpotShapeAnalyzerFactory.PERIMETER, perimeter );
 		spot.putFeature( SpotShapeAnalyzerFactory.CIRCULARITY, circularity );
 		spot.putFeature( SpotShapeAnalyzerFactory.SOLIDITY, solidity );
+		spot.putFeature( SpotShapeAnalyzerFactory.SHAPE_INDEX, shapeIndex );
 	}
 
 	private static final double getLength( final SpotRoi roi )

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

@@ -46,9 +46,10 @@ public class SpotShapeAnalyzerFactory< T extends RealType< T > & NativeType< T >
 	public static final String PERIMETER = "PERIMETER";
 	public static final String CIRCULARITY = "CIRCULARITY";
 	public static final String SOLIDITY = "SOLIDITY";
+	public static final String SHAPE_INDEX = "SHAPE_INDEX";
 
 	private static final List< String > FEATURES = Arrays.asList( new String[] {
-			AREA, PERIMETER, CIRCULARITY, SOLIDITY } );
+			AREA, PERIMETER, CIRCULARITY, SOLIDITY, SHAPE_INDEX } );
 	private static final Map< String, String > FEATURE_SHORTNAMES = new HashMap< >();
 	private static final Map< String, String > FEATURE_NAMES = new HashMap< >();
 	private static final Map< String, Dimension > FEATURE_DIMENSIONS = new HashMap< >();
@@ -59,24 +60,27 @@ public class SpotShapeAnalyzerFactory< T extends RealType< T > & NativeType< T >
 		FEATURE_SHORTNAMES.put( PERIMETER, "Perim." );
 		FEATURE_SHORTNAMES.put( CIRCULARITY, "Circ." );
 		FEATURE_SHORTNAMES.put( SOLIDITY, "Solidity" );
+		FEATURE_SHORTNAMES.put( SHAPE_INDEX, "Shape index" );
 
 		FEATURE_NAMES.put( AREA, "Area" );
 		FEATURE_NAMES.put( PERIMETER, "Perimeter" );
 		FEATURE_NAMES.put( CIRCULARITY, "Circularity" );
 		FEATURE_NAMES.put( SOLIDITY, "Solidity" );
+		FEATURE_NAMES.put( SHAPE_INDEX, "Shape index" );
 
 		FEATURE_DIMENSIONS.put( AREA, Dimension.AREA );
 		FEATURE_DIMENSIONS.put( PERIMETER, Dimension.LENGTH );
 		FEATURE_DIMENSIONS.put( CIRCULARITY, Dimension.NONE );
 		FEATURE_DIMENSIONS.put( SOLIDITY, Dimension.NONE );
+		FEATURE_DIMENSIONS.put( SHAPE_INDEX, Dimension.NONE );
 
 		FEATURE_ISINTS.put( AREA, Boolean.FALSE );
 		FEATURE_ISINTS.put( PERIMETER, Boolean.FALSE );
 		FEATURE_ISINTS.put( CIRCULARITY, Boolean.FALSE );
 		FEATURE_ISINTS.put( SOLIDITY, Boolean.FALSE );
+		FEATURE_ISINTS.put( SHAPE_INDEX, Boolean.FALSE );
 	}
 
-
 	@Override
 	public SpotAnalyzer< T > getAnalyzer( final ImgPlus< T > img, final int frame, final int channel )
 	{