add new methods

segment-anything-models-java · Nov 30, 2024 · 321475d · 321475d
1 parent d01c08e
commit 321475d
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Showing 2 changed files with 71 additions and 3 deletions.
diff --git a/src/main/java/ai/nets/samj/ij/ui/Consumer.java b/src/main/java/ai/nets/samj/ij/ui/Consumer.java
@@ -31,6 +31,7 @@
 import ij.gui.PolygonRoi;
 import ij.gui.Roi;
 import ij.gui.Toolbar;
+import ij.plugin.CompositeConverter;
 import ij.plugin.OverlayLabels;
 import ij.plugin.frame.RoiManager;
 import io.bioimage.modelrunner.system.PlatformDetection;
@@ -39,7 +40,10 @@
 import net.imglib2.Localizable;
 import net.imglib2.Point;
 import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.Img;
 import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 
 /**
@@ -209,6 +213,71 @@ public void deselectImage() {
 		this.activeWindow = null;
 	}
 
+	@Override
+	public Object getFocusedImage() {
+		return IJ.getImage();
+	}
+
+	@Override
+	public <T extends RealType<T> & NativeType<T>> RandomAccessibleInterval<T> getFocusedImageAsRai() {
+		ImagePlus imp = IJ.getImage();
+		boolean isColorRGB = imp.getType() == ImagePlus.COLOR_RGB;
+		Img<T> image = ImageJFunctions.wrap(isColorRGB ? CompositeConverter.makeComposite(imp) : imp);
+		return image;
+	}
+
+	@Override
+	public List<Rectangle> getRectRoisOnFocusImage() {
+		Roi roi = IJ.getImage().getRoi();
+		List<Rectangle> list = getRectRoisFromRoiManager();
+		if (roi == null)
+			return list;
+		if (roi.getType() != Roi.RECTANGLE)
+			return list;
+		list.add(roi.getBounds());
+		return list;
+	}
+
+	private List<Rectangle> getRectRoisFromRoiManager() {
+		List<Rectangle> list = new ArrayList<Rectangle>();
+		Roi[] rois = RoiManager.getInstance().getRoisAsArray();
+		if (rois.length == 0)
+			return list;
+		list = Arrays.stream(rois).filter(rr -> rr.getType() != Roi.RECTANGLE)
+				.map(rr -> rr.getBounds()).collect(Collectors.toList());
+		return list;
+	}
+
+	@Override
+	public List<long[]> getPointRoisOnFocusImage() {
+		Roi roi = IJ.getImage().getRoi();
+		List<long[]> list = getPointRoisFromRoiManager();
+		if (roi == null)
+			return list;
+		if (roi.getType() != Roi.POINT)
+			return list;
+		while (roi.iterator().hasNext()) {
+			java.awt.Point p = roi.iterator().next();
+			list.add(new long[] {(long) p.getX(), (long) p.getY()});
+		}
+		return list;
+	}
+
+	private List<long[]> getPointRoisFromRoiManager() {
+		List<long[]> list = new ArrayList<long[]>();
+		Roi[] rois = RoiManager.getInstance().getRoisAsArray();
+		if (rois.length == 0)
+			return list;
+		List<Roi> roiList = Arrays.stream(rois).filter(rr -> rr.getType() != Roi.POINT).collect(Collectors.toList());
+		for (Roi rr : roiList) {
+			while (rr.iterator().hasNext()) {
+				java.awt.Point p = rr.iterator().next();
+				list.add(new long[] {(long) p.getX(), (long) p.getY()});
+			}
+		}
+		return list;
+	}
+
 	@Override
 	/**
 	 * when the plugin is closed, close everything

diff --git a/src/main/java/ai/nets/samj/ij/ui/IJComboBoxItem.java b/src/main/java/ai/nets/samj/ij/ui/IJComboBoxItem.java
@@ -28,7 +28,6 @@
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.NativeType;
 import net.imglib2.type.numeric.RealType;
-import net.imglib2.util.Cast;
 
 /**
  * Implementation of the SAMJ interface {@link ComboBoxItem} that provides the SAMJ GUI
@@ -75,8 +74,8 @@ public String getImageName() {
 	public <T extends RealType<T> & NativeType<T>> RandomAccessibleInterval<T> getImageAsImgLib2() {
 		ImagePlus imp = (ImagePlus) this.getValue();
 		boolean isColorRGB = imp.getType() == ImagePlus.COLOR_RGB;
-		Img<?> image = ImageJFunctions.wrap(isColorRGB ? CompositeConverter.makeComposite(imp) : imp);
-		return Cast.unchecked(image);
+		Img<T> image = ImageJFunctions.wrap(isColorRGB ? CompositeConverter.makeComposite(imp) : imp);
+		return image;
 	}