update the interface

segment-anything-models-java · Apr 20, 2024 · 365c221 · 365c221
1 parent e2ef3b8
commit 365c221
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diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientSAM.java b/src/main/java/ai/nets/samj/communication/model/EfficientSAM.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -156,6 +157,25 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML0.java b/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML0.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -158,6 +159,22 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML1.java b/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML1.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -160,6 +161,22 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML2.java b/src/main/java/ai/nets/samj/communication/model/EfficientViTSAML2.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -160,6 +161,22 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientViTSAMXL0.java b/src/main/java/ai/nets/samj/communication/model/EfficientViTSAMXL0.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -160,6 +161,22 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/EfficientViTSAMXL1.java b/src/main/java/ai/nets/samj/communication/model/EfficientViTSAMXL1.java
@@ -27,6 +27,7 @@
 import net.imglib2.util.Cast;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 import java.util.stream.Collectors;
@@ -161,6 +162,22 @@ public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<
 		}
 	}
 
+	@Override
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D,
+			Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException {
+		try {
+			List<int[]> list = listOfPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			List<int[]> negList = listOfNegPoints2D.stream()
+					.map(i -> new int[] {(int) i.positionAsDoubleArray()[0], (int) i.positionAsDoubleArray()[1]}).collect(Collectors.toList());
+			if (negList.size() == 0) return efficientSamJ.processPoints(list, zoomedRectangle, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, zoomedRectangle, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
 	@Override
 	/**
 	 * {@inheritDoc}

diff --git a/src/main/java/ai/nets/samj/communication/model/SAMModel.java b/src/main/java/ai/nets/samj/communication/model/SAMModel.java
@@ -20,6 +20,7 @@
 package ai.nets.samj.communication.model;
 
 import java.awt.Polygon;
+import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.List;
 
@@ -98,6 +99,22 @@ public interface SAMModel {
 	 */
 	List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D) throws IOException, RuntimeException, InterruptedException;
 
+	/**
+	 * Get a 2D segmentation/annotation using two lists of points as the prompts. 
+	 * @param listOfPoints2D
+	 * 	List of points that make reference to the instance of interest
+	 * @param listOfNegPoints2D
+	 * 	list of points that makes reference to something that is not the instance of interest. This
+	 * 	points make reference to the background
+	 * @param zoomedRectangle
+	 * 	rectangle that specifies the area that is being zoomed in.It will be the area encoded.
+	 * @return a list of polygons that represent the edges of each of the masks segmented by the model
+	 * @throws IOException if any of the files needed to run the Python script is missing 
+	 * @throws RuntimeException if there is any error running the Python process
+	 * @throws InterruptedException if the process in interrupted
+	 */
+	List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D, Rectangle zoomedRectangle) throws IOException, RuntimeException, InterruptedException;
+
 	/**
 	 * Get a 2D segmentation/annotation using a bounding box as the prompt. 
 	 * @param boundingBox2D