Merge pull request #42 from ajay1685/main

Fix ROI conversion from instance segmentation mask

Author: petebankhead

build.gradle.kts

@@ -5,7 +5,7 @@ plugins {
 
 qupathExtension {
 	name = "qupath-extension-djl"
-	version = "0.4.0"
+	version = "0.4.1-SNAPSHOT"
 	group = "io.github.qupath"
 	description = "QuPath extension to use Deep Java Library"
 	automaticModule = "qupath.extension.djl"

src/main/java/qupath/ext/djl/DjlZoo.java

@@ -16,32 +16,6 @@
 
 package qupath.ext.djl;
 
-import java.awt.image.BandedSampleModel;
-import java.awt.image.BufferedImage;
-import java.awt.image.DataBufferFloat;
-import java.awt.image.WritableRaster;
-import java.io.IOException;
-import java.lang.reflect.Type;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.UUID;
-import java.util.concurrent.ConcurrentHashMap;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
-import ai.djl.repository.MRL;
-import org.locationtech.jts.geom.util.AffineTransformation;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import ai.djl.Application;
 import ai.djl.MalformedModelException;
 import ai.djl.Model;
@@ -55,13 +29,14 @@
 import ai.djl.modality.cv.output.DetectedObjects;
 import ai.djl.modality.cv.output.DetectedObjects.DetectedObject;
 import ai.djl.modality.cv.output.Joints;
-import ai.djl.ndarray.NDList;
-import ai.djl.ndarray.types.LayoutType;
-import ai.djl.ndarray.types.Shape;
 import ai.djl.modality.cv.output.Landmark;
 import ai.djl.modality.cv.output.Mask;
 import ai.djl.modality.cv.translator.BigGANTranslator;
+import ai.djl.ndarray.NDList;
+import ai.djl.ndarray.types.LayoutType;
+import ai.djl.ndarray.types.Shape;
 import ai.djl.repository.Artifact;
+import ai.djl.repository.MRL;
 import ai.djl.repository.zoo.Criteria;
 import ai.djl.repository.zoo.ModelNotFoundException;
 import ai.djl.repository.zoo.ModelZoo;
@@ -72,6 +47,9 @@
 import ai.djl.util.ClassLoaderUtils;
 import ai.djl.util.Pair;
 import ai.djl.util.PairList;
+import org.locationtech.jts.geom.util.AffineTransformation;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import qupath.lib.analysis.images.ContourTracing;
 import qupath.lib.analysis.images.SimpleImage;
 import qupath.lib.geom.Point2;
@@ -95,6 +73,27 @@
 import qupath.lib.roi.RoiTools;
 import qupath.lib.roi.interfaces.ROI;
 
+import java.awt.image.BandedSampleModel;
+import java.awt.image.BufferedImage;
+import java.awt.image.DataBufferFloat;
+import java.awt.image.WritableRaster;
+import java.io.IOException;
+import java.lang.reflect.Type;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.UUID;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
 /**
  * Helper class for working with DeepJavaLibrary model zoos.
  * 
@@ -316,13 +315,13 @@ private static TranslatorFactory getTranslatorFactory(String factoryClass) {
 	 * @return
 	 */
 	public static ROI createROI(DetectedObject obj, ImageRegion region) {
-		var box = obj.getBoundingBox();
-		if (box instanceof Mask) {
-			return createROI((Mask)box, region, 0.5);
-		} else if (box instanceof Landmark) {
-			return createROI((Landmark)box, region);
+		BoundingBox box = obj.getBoundingBox();
+		if (box instanceof Mask mask) {
+			return createROI(mask, region, 0.5);
+		} else if (box instanceof Landmark landmark) {
+			return createROI(landmark, region);
 		} else
-			return createROI((BoundingBox)box, region);
+			return createROI(box, region);
 	}
 
 	/**
@@ -335,17 +334,21 @@ public static ROI createROI(BoundingBox box, ImageRegion region) {
 		var bounds = box.getBounds();
 		double xo = 0.0;
 		double yo = 0.0;
+		double xScale = 1.0;
+		double yScale = 1.0;
 		var plane = ImagePlane.getDefaultPlane();
 		if (region != null) {
 			plane = region.getImagePlane();
 			xo = region.getMinX();
 			yo = region.getMinY();
+			xScale = region.getWidth();
+			yScale = region.getHeight();
 		}
 		return ROIs.createRectangleROI(
-				xo + bounds.getX() * region.getWidth(),
-				yo + bounds.getY() * region.getHeight(),
-				bounds.getWidth()  * region.getWidth(),
-				bounds.getHeight() * region.getHeight(),
+				xo + bounds.getX() * xScale,
+				yo + bounds.getY() * yScale,
+				bounds.getWidth()  * xScale,
+				bounds.getHeight() * yScale,
 				plane);
 	}
 
@@ -358,17 +361,16 @@ public static ROI createROI(BoundingBox box, ImageRegion region) {
 	 */
 	public static ROI createROI(Mask mask, ImageRegion region, double threshold) {
 		float[][] probs = mask.getProbDist();
-		int w = probs.length;
-		int h = probs[0].length;
+		int h = probs.length;
+		int w = probs[0].length;
 		var buffer = new DataBufferFloat(w * h, 1);
 		var sampleModel = new BandedSampleModel(buffer.getDataType(), w, h, 1);
 		var raster = WritableRaster.createWritableRaster(sampleModel, buffer, null);
-		for (int x = 0; x < w; x++) {
-			float[] col = probs[x];
-			for (int y = 0; y < h; y++) {
-				raster.setSample(x, y, 0, col[y]);
-			}
-		}
+        for (int y = 0; y < h; y++) {
+            for (int x = 0; x < w; x++) {
+                raster.setSample(x, y, 0, probs[y][x]);
+            }
+        }
 		if (region == null)
 			region = ImageRegion.createInstance(0, 0, w, h, 0, 0);
 		var geometry = ContourTracing.createTracedGeometry(raster, threshold, Double.POSITIVE_INFINITY, 0, null);
@@ -377,8 +379,10 @@ public static ROI createROI(Mask mask, ImageRegion region, double threshold) {
 
 		var transform = new AffineTransformation();
 		transform.scale(1.0/raster.getWidth(), 1.0/raster.getHeight());
-		transform.scale(bounds.getWidth(), bounds.getHeight());
-		transform.translate(bounds.getX(), bounds.getY());
+        if(!mask.isFullImageMask()) {
+            transform.scale(bounds.getWidth(), bounds.getHeight());
+            transform.translate(bounds.getX(), bounds.getY());
+        }
 		transform.scale(region.getWidth(), region.getHeight());
 		transform.translate(region.getX(), region.getY());