Use of multithreaded Otsu (ImgLib2 histogram) instead of JBM Otsu

src/main/java/fr/pasteur/ida/zellige/utils/LocalOtsu.java

@@ -37,7 +37,7 @@ public class LocalOtsu
         private final Img< T > source;
         private final Img< T > output;
         private final Img< BitType > binary;
-        private double percent;
+        private final double percent;
 
         private OtsuThreshold( final Img< T > source, final Img< BitType > binary, double percent )
         {
@@ -64,12 +64,11 @@ public class LocalOtsu
         public static < T extends RealType< T > & NativeType< T > > void
         computeLocalThreshold( Img< T > source, Img< T > output )
         {
-
             long X = source.dimension( 0 );
             long Y = source.dimension( 1 );
             long Z = source.dimension( 2 );
             List< Interval > intervals = Grids.collectAllContainedIntervals( new long[]{ X, Y, Z },
-                    new int[]{ 50, 50, 5 } );//TODO Size of a grid cube ?
+                    new int[]{ 50, 50, 3 } );//TODO Size of a grid cube ?
 
             for ( Interval interval : intervals )
             {
@@ -82,9 +81,9 @@ public class LocalOtsu
         public static < T extends RealType< T > & NativeType< T > > void
         applyLocalThreshold( Img< T > source, Img< T > output, Img<BitType> binary , double percent)
         {
-            ImageJFunctions.show( output, "grid" );
-            double threshold = Otsu.getThreshold( source ).getRealDouble();
+            double threshold = Threshold.getThreshold( source, percent ).getRealDouble();
             Utils.gaussConvolution( output.copy(), output, new double[]{5, 5, 1} );
+            ImageJFunctions.show( output.copy(), "grid" );
             Cursor<T> sourceCursor = source.localizingCursor();
             Cursor<T> outputCursor = output.cursor();
             RandomAccess< BitType > randomAccess = binary.randomAccess();
@@ -94,12 +93,15 @@ public class LocalOtsu
                 outputCursor.fwd();
                 final float s = sourceCursor.get().getRealFloat();
                 final float o = outputCursor.get().getRealFloat();
-                if (s >= Math.max( o, threshold* percent))// background substraction
                 {
-                   randomAccess.setPosition( sourceCursor );
-                   randomAccess.get().set(true);
+                if (s >= Math.max( o, threshold))// background subtraction
+                    {
+                        randomAccess.setPosition( sourceCursor );
+                        randomAccess.get().set( true );
+                    }
                 }
             }
+            ImageJFunctions.show( binary, "binary" );
         }