add missing method

segment-anything-models-java · Aug 7, 2024 · d6fc080 · d6fc080
1 parent fc7258a
commit d6fc080
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Showing 8 changed files with 62 additions and 54 deletions.
diff --git a/src/main/java/ai/nets/samj/install/EfficientSamEnvManager.java b/src/main/java/ai/nets/samj/install/EfficientSamEnvManager.java
@@ -294,21 +294,12 @@ public void installSAMDeps(boolean force) throws IOException, InterruptedExcepti
 			}
 			ArrayList<String> pipInstall = new ArrayList<String>();
 			for (String ss : new String[] {"-m", "pip", "install"}) pipInstall.add(ss);
-			// TODO until appose new release for (String ss : INSTALL_PIP_DEPS) pipInstall.add(ss);
-			/*
-			try {
-				Mamba.runPythonIn(Paths.get(path,  "envs", COMMON_ENV_NAME).toFile(), pipInstall.stream().toArray( String[]::new ));
-			} catch (IOException | InterruptedException e) {
-	            thread.interrupt();
-	            passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- FAILED PYTHON ENVIRONMENT CREATION WHEN INSTALLING PIP DEPENDENCIES");
-				throw e;
-			}
-			*/
 		}
         thread.interrupt();
         passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- PYTHON ENVIRONMENT CREATED");
         // TODO remove
         installApposePackage(ESAM_ENV_NAME);
+		installEfficientSAMPackage(force);
 	}
 
 	/**
@@ -428,4 +419,9 @@ public String getModelEnv() {
 	public String getModelWeigthsName() {
 		return ESAM_SMALL_WEIGHTS_NAME;
 	}
+
+	@Override
+	public String getModelWeigthPath() {
+		return Paths.get(this.path, "envs", ESAM_ENV_NAME, ESAM_NAME, "weights", ESAM_SMALL_WEIGHTS_NAME).toAbsolutePath().toString();
+	}
 }
diff --git a/src/main/java/ai/nets/samj/install/EfficientViTSamEnvManager.java b/src/main/java/ai/nets/samj/install/EfficientViTSamEnvManager.java
@@ -356,6 +356,7 @@ public void installSAMDeps(boolean force) throws IOException, InterruptedExcepti
         passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- EFFICIENTVITSAM PYTHON ENVIRONMENT CREATED");
         // TODO remove
         installApposePackage(EVITSAM_ENV_NAME);
+        installEfficientViTSAMPackage(force);
 	}
 
 	private void installOnnxsim(File envFile) throws IOException, InterruptedException {
@@ -414,7 +415,7 @@ public void installEfficientViTSAMPackage(boolean force) throws IOException, Int
 		String zipResourcePath = "efficientvit.zip";
         String outputDirectory = mamba.getEnvsDir() + File.separator + EVITSAM_ENV_NAME;
         try (
-        	InputStream zipInputStream = SamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
+        	InputStream zipInputStream = EfficientViTSamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
         	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
         		) {
         	ZipEntry entry;
@@ -492,4 +493,9 @@ public String getModelEnv() {
 	public String getModelWeigthsName() {
 		return modelType + ".pt";
 	}
+
+	@Override
+	public String getModelWeigthPath() {
+		return Paths.get(this.path, "envs", EVITSAM_ENV_NAME, EVITSAM_NAME, "weights", modelType + ".pt").toAbsolutePath().toString();
+	}
 }
diff --git a/src/main/java/ai/nets/samj/install/Sam2EnvManager.java b/src/main/java/ai/nets/samj/install/Sam2EnvManager.java
@@ -21,9 +21,7 @@
 
 import java.io.File;
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.FileOutputStream;
+import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.nio.file.Paths;
@@ -32,8 +30,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.function.Consumer;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 
 import io.bioimage.modelrunner.system.PlatformDetection;
 
@@ -379,4 +375,13 @@ public String getModelEnv() {
 	public String getModelWeigthsName() {
 		return modelType + ".pt";
 	}
+
+	@Override
+	public String getModelWeigthPath() {
+		try {
+			return Paths.get(path, "envs", SAM2_ENV_NAME, SAM2_NAME, "weights", DownloadModel.getFileNameFromURLString(String.format(SAM2_URL, modelType))).toAbsolutePath().toString();
+		} catch (MalformedURLException e) {
+			return Paths.get(path, "envs", SAM2_ENV_NAME, SAM2_NAME, "weights", String.format("sam2_hiera_%s.pt", modelType)).toAbsolutePath().toString();
+		}
+	}
 }
diff --git a/src/main/java/ai/nets/samj/install/SamEnvManagerAbstract.java b/src/main/java/ai/nets/samj/install/SamEnvManagerAbstract.java
@@ -102,6 +102,8 @@ public abstract class SamEnvManagerAbstract {
 
 	public abstract String getModelWeigthsName();
 
+	public abstract String getModelWeigthPath();
+
 	public abstract String getModelEnv();
 
 

diff --git a/...a/ai/nets/samj/install/SamEnvManager.java → .../nets/samj/install/SamEnvManager_old.java b/...a/ai/nets/samj/install/SamEnvManager.java → .../nets/samj/install/SamEnvManager_old.java
@@ -59,7 +59,7 @@
  * 
  * @author Carlos Javier Garcia Lopez de Haro
  */
-public class SamEnvManager {
+public class SamEnvManager_old {
 	/**
 	 * Name of the file that contains the weights of SAM Huge
 	 */
@@ -221,7 +221,7 @@ public class SamEnvManager {
 	 * 	the path where the corresponding micromamba shuold be installed
 	 * @return an instance of {@link SamEnvManager}
 	 */
-	public static SamEnvManager create(String path) {
+	public static SamEnvManager_old create(String path) {
 		return create(path, (ss) -> {});
 	}
 
@@ -235,8 +235,8 @@ public static SamEnvManager create(String path) {
 	 * 	an specific consumer where info about the installation is going to be communicated
 	 * @return an instance of {@link SamEnvManager}
 	 */
-	public static SamEnvManager create(String path, Consumer<String> consumer) {
-		SamEnvManager installer = new SamEnvManager();
+	public static SamEnvManager_old create(String path, Consumer<String> consumer) {
+		SamEnvManager_old installer = new SamEnvManager_old();
 		installer.path = path;
 		installer.consumer = consumer;
 		installer.mamba = new Mamba(path);
@@ -249,7 +249,7 @@ public static SamEnvManager create(String path, Consumer<String> consumer) {
 	 * Micromamba does not need to be installed as the code will install it automatically.
 	 * @return an instance of {@link SamEnvManager}
 	 */
-	public static SamEnvManager create() {
+	public static SamEnvManager_old create() {
 		return create(DEFAULT_DIR);
 	}
 
@@ -261,7 +261,7 @@ public static SamEnvManager create() {
 	 * 	an specific consumer where info about the installation is going to be communicated
 	 * @return an instance of {@link SamEnvManager}
 	 */
-	public static SamEnvManager create(Consumer<String> consumer) {
+	public static SamEnvManager_old create(Consumer<String> consumer) {
 		return create(DEFAULT_DIR, consumer);
 	}
 
@@ -442,7 +442,7 @@ public void downloadESAMSmallWeights(boolean force) throws IOException, Interrup
 		String zipResourcePath = "efficient_sam_vits.pt.zip";
         String outputDirectory = Paths.get(path, "envs", ESAM_ENV_NAME, ESAM_NAME, "weights").toFile().getAbsolutePath();
         try (
-        	InputStream zipInputStream = SamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
+        	InputStream zipInputStream = SamEnvManager_old.class.getClassLoader().getResourceAsStream(zipResourcePath);
         	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
         		) {
         	ZipEntry entry;
@@ -743,7 +743,7 @@ private void installApposePackage(String envName, boolean force) throws IOExcept
 		String zipResourcePath = "appose-python.zip";
         String outputDirectory = mamba.getEnvsDir() + File.separator + envName;
         try (
-            	InputStream zipInputStream = SamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
+            	InputStream zipInputStream = SamEnvManager_old.class.getClassLoader().getResourceAsStream(zipResourcePath);
             	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
             		) {
             	ZipEntry entry;
@@ -810,7 +810,7 @@ public void installSAMPackage(boolean force) throws IOException, InterruptedExce
 		String zipResourcePath = "SAM.zip";
         String outputDirectory = mamba.getEnvsDir() + File.separator + SAM_ENV_NAME + File.separator + SAM_NAME;
         try (
-        	InputStream zipInputStream = SamEnvManager.class.getResourceAsStream(zipResourcePath);
+        	InputStream zipInputStream = SamEnvManager_old.class.getResourceAsStream(zipResourcePath);
         	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
         		) {
         	ZipEntry entry;
@@ -873,7 +873,7 @@ public void installEfficientSAMPackage(boolean force) throws IOException, Interr
 		String zipResourcePath = "EfficientSAM.zip";
         String outputDirectory = mamba.getEnvsDir() + File.separator + ESAM_ENV_NAME;
         try (
-        	InputStream zipInputStream = SamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
+        	InputStream zipInputStream = SamEnvManager_old.class.getClassLoader().getResourceAsStream(zipResourcePath);
         	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
         		) {
         	ZipEntry entry;
@@ -931,7 +931,7 @@ public void installEfficientViTSAMPackage(boolean force) throws IOException, Int
 		String zipResourcePath = "efficientvit.zip";
         String outputDirectory = mamba.getEnvsDir() + File.separator + EVITSAM_ENV_NAME;
         try (
-        	InputStream zipInputStream = SamEnvManager.class.getClassLoader().getResourceAsStream(zipResourcePath);
+        	InputStream zipInputStream = SamEnvManager_old.class.getClassLoader().getResourceAsStream(zipResourcePath);
         	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
         		) {
         	ZipEntry entry;

diff --git a/src/main/java/ai/nets/samj/models/EfficientSamJ.java b/src/main/java/ai/nets/samj/models/EfficientSamJ.java
@@ -19,13 +19,13 @@
  */
 package ai.nets.samj.models;
 
-import ai.nets.samj.install.SamEnvManager;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import ai.nets.samj.install.EfficientSamEnvManager;
+import ai.nets.samj.install.SamEnvManagerAbstract;
 import io.bioimage.modelrunner.apposed.appose.Environment;
 import io.bioimage.modelrunner.apposed.appose.Service.Task;
 import io.bioimage.modelrunner.apposed.appose.Service.TaskStatus;
@@ -90,7 +90,7 @@ public class EfficientSamJ extends AbstractSamJ {
 	 * @throws RuntimeException if there is any error running the Python code
 	 * @throws InterruptedException if the process is interrupted
 	 */
-	private EfficientSamJ(SamEnvManager manager) throws IOException, RuntimeException, InterruptedException {
+	private EfficientSamJ(SamEnvManagerAbstract manager) throws IOException, RuntimeException, InterruptedException {
 		this(manager, (t) -> {}, false);
 	}
 
@@ -108,21 +108,21 @@ private EfficientSamJ(SamEnvManager manager) throws IOException, RuntimeExceptio
 	 * @throws InterruptedException if the process is interrupted
 	 * 
 	 */
-	private EfficientSamJ(SamEnvManager manager,
+	private EfficientSamJ(SamEnvManagerAbstract manager,
 	                      final DebugTextPrinter debugPrinter,
 	                      final boolean printPythonCode) throws IOException, RuntimeException, InterruptedException {
 
 		this.debugPrinter = debugPrinter;
 		this.isDebugging = printPythonCode;
 
 		this.env = new Environment() {
-			@Override public String base() { return manager.getEfficientSAMPythonEnv(); }
+			@Override public String base() { return manager.getModelEnv(); }
 			};
 		python = env.python();
 		python.debug(debugPrinter::printText);
 		String IMPORTS_FORMATED = String.format(IMPORTS,
-				manager.getEfficientSamEnv() + File.separator + SamEnvManager.ESAM_NAME,
-				manager.getEfficientSAMSmallWeightsPath());
+				manager.getModelEnv() + File.separator + EfficientSamEnvManager.ESAM_NAME,
+				manager.getModelWeigthPath());
 		printScript(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES, "Edges tracing code");
 		Task task = python.task(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES);
 		System.out.println(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES);
@@ -156,7 +156,7 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientSamJ
-	initializeSam(SamEnvManager manager,
+	initializeSam(SamEnvManagerAbstract manager,
 	              RandomAccessibleInterval<T> image,
 	              final DebugTextPrinter debugPrinter,
 	              final boolean printPythonCode) throws IOException, RuntimeException, InterruptedException {
@@ -191,7 +191,7 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientSamJ
-	initializeSam(SamEnvManager manager, RandomAccessibleInterval<T> image) throws IOException, RuntimeException, InterruptedException {
+	initializeSam(SamEnvManagerAbstract manager, RandomAccessibleInterval<T> image) throws IOException, RuntimeException, InterruptedException {
 		EfficientSamJ sam = null;
 		try{
 			sam = new EfficientSamJ(manager);
@@ -399,7 +399,7 @@ void adaptImageToModel(final RandomAccessibleInterval<T> ogImg, RandomAccessible
 	public static void main(String[] args) throws IOException, RuntimeException, InterruptedException {
 		RandomAccessibleInterval<UnsignedByteType> img = ArrayImgs.unsignedBytes(new long[] {50, 50, 3});
 		img = Views.addDimension(img, 1, 2);
-		try (EfficientSamJ sam = initializeSam(SamEnvManager.create(), img)) {
+		try (EfficientSamJ sam = initializeSam(EfficientSamEnvManager.create(), img)) {
 			sam.processBox(new int[] {0, 5, 10, 26});
 		}
 	}

diff --git a/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java b/src/main/java/ai/nets/samj/models/EfficientViTSamJ.java
@@ -24,7 +24,8 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import ai.nets.samj.install.SamEnvManager;
+import ai.nets.samj.install.EfficientViTSamEnvManager;
+import ai.nets.samj.install.SamEnvManagerAbstract;
 
 import java.io.File;
 import java.io.IOException;
@@ -124,7 +125,7 @@ public class EfficientViTSamJ extends AbstractSamJ {
 	 * @throws RuntimeException if there is any error running the Python code
 	 * @throws InterruptedException if the process is interrupted
 	 */
-	private EfficientViTSamJ(SamEnvManager manager, String type) throws IOException, RuntimeException, InterruptedException {
+	private EfficientViTSamJ(SamEnvManagerAbstract manager, String type) throws IOException, RuntimeException, InterruptedException {
 		this(manager, type, (t) -> {}, false);
 	}
 
@@ -144,7 +145,7 @@ private EfficientViTSamJ(SamEnvManager manager, String type) throws IOException,
 	 * @throws InterruptedException if the process is interrupted
 	 * 
 	 */
-	private EfficientViTSamJ(SamEnvManager manager, String type,
+	private EfficientViTSamJ(SamEnvManagerAbstract manager, String type,
 	                      final DebugTextPrinter debugPrinter,
 	                      final boolean printPythonCode) throws IOException, RuntimeException, InterruptedException {
 
@@ -155,13 +156,13 @@ private EfficientViTSamJ(SamEnvManager manager, String type,
 		this.isDebugging = printPythonCode;
 
 		this.env = new Environment() {
-			@Override public String base() { return manager.getEfficientViTSamEnv(); }
+			@Override public String base() { return manager.getModelEnv(); }
 			};
 		python = env.python();
 		python.debug(debugPrinter::printText);
 		IMPORTS_FORMATED = String.format(IMPORTS,
-									manager.getEfficientViTSamEnv() + File.separator + SamEnvManager.EVITSAM_NAME,
-									MODELS_DICT.get(type), MODELS_DICT.get(type), manager.getEfficientViTSAMWeightsPath(type));
+									manager.getModelEnv() + File.separator + EfficientViTSamEnvManager.EVITSAM_NAME,
+									MODELS_DICT.get(type), MODELS_DICT.get(type), manager.getModelWeigthPath());
 
 		printScript(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES, "Edges tracing code");
 		Task task = python.task(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES);
@@ -199,7 +200,7 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientViTSamJ
-	initializeSam(String modelType, SamEnvManager manager,
+	initializeSam(String modelType, SamEnvManagerAbstract manager,
 	              RandomAccessibleInterval<T> image,
 	              final DebugTextPrinter debugPrinter,
 	              final boolean printPythonCode) throws IOException, RuntimeException, InterruptedException {
@@ -234,7 +235,7 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientViTSamJ
-	initializeSam(String modelType, SamEnvManager manager, RandomAccessibleInterval<T> image) 
+	initializeSam(String modelType, SamEnvManagerAbstract manager, RandomAccessibleInterval<T> image) 
 				throws IOException, RuntimeException, InterruptedException {
 		EfficientViTSamJ sam = null;
 		try{
@@ -272,11 +273,11 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientViTSamJ
-	initializeSam(SamEnvManager manager,
+	initializeSam(SamEnvManagerAbstract manager,
 	              RandomAccessibleInterval<T> image,
 	              final DebugTextPrinter debugPrinter,
 	              final boolean printPythonCode) throws IOException, RuntimeException, InterruptedException {
-		return initializeSam(SamEnvManager.DEFAULT_EVITSAM, manager, image, debugPrinter, printPythonCode);
+		return initializeSam(EfficientViTSamEnvManager.DEFAULT_EVITSAM, manager, image, debugPrinter, printPythonCode);
 	}
 
 	/**
@@ -299,8 +300,8 @@ else if (task.status == TaskStatus.CRASHED)
 	 * @throws InterruptedException if the process is interrupted
 	 */
 	public static <T extends RealType<T> & NativeType<T>> EfficientViTSamJ
-	initializeSam(SamEnvManager manager, RandomAccessibleInterval<T> image) throws IOException, RuntimeException, InterruptedException {
-		return initializeSam(SamEnvManager.DEFAULT_EVITSAM, manager, image);
+	initializeSam(SamEnvManagerAbstract manager, RandomAccessibleInterval<T> image) throws IOException, RuntimeException, InterruptedException {
+		return initializeSam(EfficientViTSamEnvManager.DEFAULT_EVITSAM, manager, image);
 	}
 
 	@Override
@@ -496,7 +497,7 @@ void adaptImageToModel(RandomAccessibleInterval<T> ogImg, RandomAccessibleInterv
 	public static void main(String[] args) throws IOException, RuntimeException, InterruptedException {
 		RandomAccessibleInterval<UnsignedByteType> img = ArrayImgs.unsignedBytes(new long[] {50, 50, 3});
 		img = Views.addDimension(img, 1, 2);
-		try (EfficientViTSamJ sam = initializeSam(SamEnvManager.create(), img)) {
+		try (EfficientViTSamJ sam = initializeSam(EfficientViTSamEnvManager.create(), img)) {
 			sam.processBox(new int[] {0, 5, 10, 26});
 		}
 	}

diff --git a/src/main/java/ai/nets/samj/models/Sam2.java b/src/main/java/ai/nets/samj/models/Sam2.java
@@ -95,7 +95,7 @@ public class Sam2 extends AbstractSamJ {
 			+ "globals()['torch'] = torch" + System.lineSeparator()
 			+ "globals()['predictor'] = predictor" + System.lineSeparator();
 	/**
-	 * String containing the Python imports code after it has been formatted with the correct 
+	 * String containing the Python imports code after it has been formated with the correct 
 	 * paths and names
 	 */
 	private String IMPORTS_FORMATED;
@@ -147,9 +147,7 @@ private Sam2(SamEnvManagerAbstract manager, String type,
 			};
 		python = env.python();
 		python.debug(debugPrinter::printText);
-		IMPORTS_FORMATED = String.format(IMPORTS, type,
-									manager.getModelEnv() + File.separator + Sam2EnvManager.SAM2_ENV_NAME
-									+ File.separator + manager.getModelWeigthsName());
+		IMPORTS_FORMATED = String.format(IMPORTS, type, manager.getModelWeigthPath());
 
 		printScript(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES, "Edges tracing code");
 		Task task = python.task(IMPORTS_FORMATED + PythonMethods.TRACE_EDGES);
Original file line number	Diff line number	Diff line change
Expand Up		@@ -102,6 +102,8 @@ public abstract class SamEnvManagerAbstract {

		public abstract String getModelWeigthsName();

		public abstract String getModelWeigthPath();

		public abstract String getModelEnv();


Expand Down