add possibility of crops of the image

src/main/java/ai/nets/samj/annotation/Mask.java

@@ -20,6 +20,7 @@
 package ai.nets.samj.annotation;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.util.Arrays;
 import java.util.List;
 
@@ -40,13 +41,16 @@ public class Mask {
 
 	private final long[] rleEncoding;
 
-	private Mask(Polygon contour, long[] rleEncoding) {
+	private final Rectangle crop;
+
+	private Mask(Polygon contour, long[] rleEncoding, Rectangle crop) {
 		this.contour = contour;
 		this.rleEncoding = rleEncoding;
+		this.crop = crop;
 	}
 
-	public static Mask build(Polygon contour, long[] rleEncoding) {
-		return new Mask(contour, rleEncoding);
+	public static Mask build(Polygon contour, long[] rleEncoding, Rectangle crop) {
+		return new Mask(contour, rleEncoding, crop);
 	}
 
 	public Polygon getContour() {
@@ -72,7 +76,8 @@ public static RandomAccessibleInterval<UnsignedByteType> getMask(long width, lon
 
 		for (Mask mask : masks) {
 			for (int i = 0; i < mask.getRLEMask().length; i += 2) {
-				int start = (int) mask.getRLEMask()[i];
+				int cropStart = mask.crop.x;
+				int start = cropStart + (int) mask.getRLEMask()[i];
 				int len = (int) mask.getRLEMask()[i+ 1];
 				Arrays.fill(arr, start, start + len, (byte) 1);
 			}