correct bugs

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

@@ -20,7 +20,6 @@
 package ai.nets.samj.annotation;
 
 import java.awt.Polygon;
-import java.awt.Rectangle;
 import java.util.Arrays;
 import java.util.List;
 
@@ -41,16 +40,13 @@ public class Mask {
 
 	private final long[] rleEncoding;
 
-	private final Rectangle crop;
-
-	private Mask(Polygon contour, long[] rleEncoding, Rectangle crop) {
+	private Mask(Polygon contour, long[] rleEncoding) {
 		this.contour = contour;
 		this.rleEncoding = rleEncoding;
-		this.crop = crop;
 	}
 
-	public static Mask build(Polygon contour, long[] rleEncoding, Rectangle crop) {
-		return new Mask(contour, rleEncoding, crop);
+	public static Mask build(Polygon contour, long[] rleEncoding) {
+		return new Mask(contour, rleEncoding);
 	}
 
 	public Polygon getContour() {
@@ -77,9 +73,7 @@ public static RandomAccessibleInterval<UnsignedByteType> getMask(long width, lon
 		for (Mask mask : masks) {
 			long[] rle = mask.getRLEMask();
 			for (int i = 0; i < rle.length; i += 2) {
-				int cropStartx = mask.crop.x;
-				int cropStarty = mask.crop.y;
-				int start = (int) (width * (cropStarty + i / 2) + cropStartx + mask.getRLEMask()[i]);
+				int start = (int) mask.getRLEMask()[i];
 				int len = (int) mask.getRLEMask()[i+ 1];
 				Arrays.fill(arr, start, start + len, (byte) 1);
 			}

src/main/java/ai/nets/samj/models/AbstractSamJ.java

@@ -371,7 +371,7 @@ else if (task.outputs.get("contours_x") == null)
 				throw new RuntimeException();
 			else if (task.outputs.get("contours_y") == null)
 				throw new RuntimeException();
-			else if (task.outputs.get("rles") == null)
+			else if (task.outputs.get("rle") == null)
 				throw new RuntimeException();
 			results = task.outputs;
 		} catch (IOException | InterruptedException | RuntimeException e) {
@@ -393,7 +393,7 @@ else if (task.outputs.get("rles") == null)
 			int[] xArr = contours_x.next().stream().mapToInt(Number::intValue).toArray();
 			int[] yArr = contours_y.next().stream().mapToInt(Number::intValue).toArray();
 			long[] rle = rles.next().stream().mapToLong(Number::longValue).toArray();
-			masks.add(Mask.build(new Polygon(xArr, yArr, xArr.length), rle, cropRect));
+			masks.add(Mask.build(new Polygon(xArr, yArr, xArr.length), rle));
 		}
 		return masks;
 	}
@@ -1034,15 +1034,19 @@ protected long[] calculateEncodingNewCoords(int[] boundingBox, long[] imageSize)
 	 * to detect small objects compared to the size of the whole image, SAMJ might encode crops of
 	 * the total image, thus the coordinates of the polygons obtained need to be shifted in order
 	 * to match the original image.
-	 * @param polys
-	 * 	polys obtained by SAMJ on the encoded crop
+	 * @param masks
+	 * 	masks obtained by SAMJ on the encoded crop
 	 * @param encodeCoords
 	 * 	position of the crop in the total image
 	 */
-	protected void recalculatePolys(List<Mask> polys, long[] encodeCoords) {
-		polys.stream().forEach(pp -> {
+	protected void recalculatePolys(List<Mask> masks, long[] encodeCoords) {
+		masks.stream().forEach(pp -> {
 			pp.getContour().xpoints = Arrays.stream(pp.getContour().xpoints).map(x -> x + (int) encodeCoords[0]).toArray();
 			pp.getContour().ypoints = Arrays.stream(pp.getContour().ypoints).map(y -> y + (int) encodeCoords[1]).toArray();
+			for (int i = 0; i < pp.getRLEMask().length; i += 2) {
+				pp.getRLEMask()[i] = encodeCoords[0] + pp.getRLEMask()[i] % this.targetDims[0] 
+						+ (((int) (pp.getRLEMask()[i] / this.targetDims[0])) + encodeCoords[1]) * this.targetDims[0];
+			}
 		});
 	}
 

src/main/java/ai/nets/samj/models/PythonMethods.java

@@ -92,7 +92,7 @@ public class PythonMethods {
 			+ "            rle = encode_rle(obj.image)" + System.lineSeparator()
 			+ "            bbox_w = obj.bbox[3] - obj.bbox[1]" + System.lineSeparator()
 			+ "            for i in range(0, len(rle), 2):" + System.lineSeparator()
-			+ "              rle[i] = sam_result.shape[1] * (obj.bbox[0] - 1 + rle[i] // bbox_w) + obj.bbox[1] + rle[i] % bbox_w" + System.lineSeparator()
+			+ "              rle[i] = sam_result.shape[1] * (obj.bbox[0] + rle[i] // bbox_w) + obj.bbox[1] + rle[i] % bbox_w" + System.lineSeparator()
 			+ "            rles.append(rle)" + System.lineSeparator()
 			+ "            x_contours.append(x_coords)" + System.lineSeparator()
 			+ "            y_contours.append(y_coords)" + System.lineSeparator()