add sam 2 models

src/main/java/ai/nets/samj/communication/model/SAM2Small.java

@@ -0,0 +1,281 @@
+/*-
+ * #%L
+ * Library to call models of the family of SAM (Segment Anything Model) from Java
+ * %%
+ * Copyright (C) 2024 SAMJ developers.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package ai.nets.samj.communication.model;
+
+import net.imglib2.Interval;
+import net.imglib2.Localizable;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+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;
+
+import ai.nets.samj.models.AbstractSamJ;
+import ai.nets.samj.models.Sam2;
+import ai.nets.samj.install.Sam2EnvManager;
+import ai.nets.samj.install.SamEnvManagerAbstract;
+import ai.nets.samj.ui.SAMJLogger;
+
+/**
+ * Instance to communicate with EfficientSAM
+ * @author Carlos Garcia Lopez de Haro
+ * @author Vladimir Ulman
+ */
+public class SAM2Small implements SAMModel {
+
+	private Sam2 efficientSamJ;
+	private final SamEnvManagerAbstract manager;
+	private SAMJLogger log;
+	private Boolean installed = false;
+	private boolean onlyBiggest = false;
+	/**
+	 * Name of the model
+	 */
+	public static final String FULL_NAME = "SAM2 Small";
+	/**
+	 * Axes order required for the input image by the model
+	 */
+	public static final String INPUT_IMAGE_AXES = "xyc";
+
+	private static final String HTML_DESCRIPTION = "SAM-2: Segment Anything Model 2 <br>"
+	        + "<strong>Weights size:</strong> 184.3 MB <br>"
+	        + "<strong>Speed:</strong> 6th out of 6 <br>"
+	        + "<strong>Performance:</strong> 1st out of 6 <br>"
+	        + "<strong>GitHub Repository:</strong> <a href=\"https://github.com/facebookresearch/segment-anything-2\">https://github.com/facebookresearch/segment-anything-2</a> <br>"
+	        + "<strong>Paper:</strong> <a href=\"https://ai.meta.com/research/publications/sam-2-segment-anything-in-images-and-videos/\">SAM 2: Segment Anything in Images and Videos\n"
+	        + "Anything</a>";
+
+	private static final String CAUTION_STRING = "<br><p style=\"color: green;\">CAUTION: This model is computationally heavy. It is not recommended to use it on lower-end computers.</p>";
+
+
+	/**
+	 * Create an instance of the model that loads the model and encodes an image
+	 * @param image
+	 * 	the image to be encoded
+	 * @param log
+	 * 	a logging functional interface to be able to keep track of what the model is doing
+	 * @throws IOException if any of the files to run a Python process is missing
+	 * @throws RuntimeException if there is any error running the Python code
+	 * @throws InterruptedException if the process is interrupted
+	 */
+	public SAM2Small() throws IOException, RuntimeException, InterruptedException {
+		this.manager = Sam2EnvManager.create(Sam2EnvManager.DEFAULT_DIR, "small");
+		efficientSamJ = Sam2.initializeSam("small", manager);
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public String getName() {
+		return FULL_NAME;
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public String getDescription() {
+		return HTML_DESCRIPTION + (!this.installed ? SAMModel.HTML_NOT_INSTALLED : CAUTION_STRING);
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public boolean isInstalled() {
+		return installed;
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public void setImage(final RandomAccessibleInterval<?> image, final SAMJLogger useThisLoggerForIt) 
+			throws IOException, InterruptedException, RuntimeException {
+		if (this.efficientSamJ == null)
+			efficientSamJ = Sam2.initializeSam("small", manager);
+		try {
+			this.log = useThisLoggerForIt;
+			AbstractSamJ.DebugTextPrinter filteringLogger = text -> {
+				int idx = text.indexOf("contours_x");
+				if (idx > 0) this.log.info( text.substring(0,idx) );
+				else this.log.info( text );
+			};
+			this.efficientSamJ.setDebugPrinter(filteringLogger);
+			this.efficientSamJ.setImage(Cast.unchecked(image));;
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME + " experienced an error: " + e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public void setInstalled(boolean installed) {
+		this.installed = installed;		
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public List<Polygon> fetch2dSegmentation(List<Localizable> listOfPoints2D, List<Localizable> listOfNegPoints2D) 
+			throws IOException, InterruptedException, RuntimeException {
+		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, !onlyBiggest);
+			else return efficientSamJ.processPoints(list, negList, !onlyBiggest);
+		} catch (IOException | RuntimeException | InterruptedException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@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}
+	 */
+	public List<Polygon> fetch2dSegmentation(Interval boundingBox2D) 
+			throws IOException, InterruptedException, RuntimeException {
+		try {
+			//order to processBox() should be: x0,y0, x1,y1
+			final int bbox[] = {
+				(int)boundingBox2D.min(0),
+				(int)boundingBox2D.min(1),
+				(int)boundingBox2D.max(0),
+				(int)boundingBox2D.max(1)
+			};
+			return efficientSamJ.processBox(bbox, !onlyBiggest);
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public <T extends RealType<T> & NativeType<T>> List<Polygon> fetch2dSegmentationFromMask(RandomAccessibleInterval<T> rai) 
+			throws IOException, InterruptedException, RuntimeException {
+		try {
+			return efficientSamJ.processMask(rai, !onlyBiggest);
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME+", providing empty result because of some trouble: "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public void notifyUiHasBeenClosed() {
+		log.info(FULL_NAME+": OKAY, I'm closing myself...");
+		closeProcess();
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public void closeProcess() {
+		efficientSamJ.close();
+		efficientSamJ = null;
+	}
+
+	@Override
+	/**
+	 * {@inheritDoc}
+	 */
+	public String getInputImageAxes() {
+		return INPUT_IMAGE_AXES;
+	}
+
+	@Override
+	public void setReturnOnlyBiggest(boolean onlyBiggest) {
+		this.onlyBiggest = onlyBiggest;
+	}
+
+	@Override
+	public String persistEncoding() throws IOException, InterruptedException {
+		try {
+			return efficientSamJ.persistEncoding();
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME+", unable to persist the encoding: "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	public void selectEncoding(String encodingName) throws IOException, InterruptedException {
+		try {
+			efficientSamJ.selectEncoding(encodingName);
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME+", unable to persist the encoding named '" + encodingName + "': "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	public void deleteEncoding(String encodingName) throws IOException, InterruptedException {
+		try {
+			efficientSamJ.deleteEncoding(encodingName);
+		} catch (IOException | InterruptedException | RuntimeException e) {
+			log.error(FULL_NAME+", unable to delete the encoding named '" + encodingName + "': "+e.getMessage());
+			throw e;
+		}
+	}
+
+	@Override
+	public SamEnvManagerAbstract getInstallationManger() {
+		return this.manager;
+	}
+}