create abstract class to install sam models and start adding sam2

src/main/java/ai/nets/samj/install/SamEnvManager.java

@@ -65,13 +65,17 @@ public class SamEnvManager {
 	 */
 	final public static String SAM_WEIGHTS_NAME = "sam_vit_h_4b8939.pth";
 	/**
-	 * Name of the file that contains the weights for EfficientSAM small
+	 * Name of the file that contains the weights of SAM Huge
 	 */
-	final public static String ESAM_SMALL_WEIGHTS_NAME ="efficient_sam_vits.pt";
+	final public static String SAM2_TINY_WEIGHTS_NAME = "sam_vit_h_4b8939.pth";
+	/**
+	 * Name of the file that contains the weights of SAM Huge
+	 */
+	final public static String SAM2_SMALL_WEIGHTS_NAME = "sam_vit_h_4b8939.pth";
 	/**
-	 * Name of the encoder (ViT Huge) that is going to be used for SAM in SAMJ
+	 * Name of the file that contains the weights for EfficientSAM small
 	 */
-	final public static String SAM_MODEL_TYPE = "vit_h";
+	final public static String ESAM_SMALL_WEIGHTS_NAME ="efficient_sam_vits.pt";
 	/**
 	 * Default version for the family of EfficientViTSAM models
 	 */

src/main/java/ai/nets/samj/install/SamEnvManagerAbstract.java

@@ -0,0 +1,277 @@
+/*-
+ * #%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.install;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.FileOutputStream;
+import java.net.HttpURLConnection;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.channels.Channels;
+import java.nio.channels.ReadableByteChannel;
+import java.nio.file.Paths;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.function.Consumer;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import io.bioimage.modelrunner.bioimageio.download.DownloadModel;
+import io.bioimage.modelrunner.engine.installation.FileDownloader;
+import io.bioimage.modelrunner.system.PlatformDetection;
+import io.bioimage.modelrunner.utils.CommonUtils;
+
+import org.apache.commons.compress.archivers.ArchiveException;
+
+import ai.nets.samj.models.EfficientViTSamJ;
+import io.bioimage.modelrunner.apposed.appose.Mamba;
+import io.bioimage.modelrunner.apposed.appose.MambaInstallException;
+import io.bioimage.modelrunner.apposed.appose.MambaInstallerUtils;
+
+/*
+ * Class that is manages the installation of SAM and EfficientSAM together with Python, their corresponding environments
+ * and dependencies
+ * 
+ * @author Carlos Javier Garcia Lopez de Haro
+ */
+public abstract class SamEnvManagerAbstract {
+
+
+	public abstract void checkSAMDepsInstalled();
+
+	public abstract void installSAMDeps();
+
+	public abstract void checkModelWeightsInstalled();
+
+	public abstract void installModelWeigths();
+
+
+
+
+	/**
+	 * Send information as Strings to the consumer
+	 * @param str
+	 * 	String that is going to be sent to the consumer
+	 */
+	private void passToConsumer(String str) {
+		consumer.accept(str);
+		millis = System.currentTimeMillis();
+	}
+
+	/**
+	 * Check whether micromamba is installed or not in the directory of the {@link SamEnvManagerAbstract} instance.
+	 * @return whether micromamba is installed or not in the directory of the {@link SamEnvManagerAbstract} instance.
+	 */
+	public boolean checkMambaInstalled() {
+		File ff = new File(path + MAMBA_RELATIVE_PATH);
+		if (!ff.exists()) return false;
+		return mamba.checkMambaInstalled();
+	}
+
+	// TODO move this to mamba
+	private void installOnnxsim(File envFile) throws IOException, InterruptedException {
+		final List< String > cmd = new ArrayList<>();
+		if ( PlatformDetection.isWindows() )
+			cmd.addAll( Arrays.asList( "cmd.exe", "/c" ) );
+		cmd.add( Paths.get( envFile.getAbsolutePath(), (PlatformDetection.isWindows() ? "python.exe" : "bin/python") ).toAbsolutePath().toString() );
+		cmd.addAll( Arrays.asList( new String[] {"-m", "pip", "install"} ) );
+		// TODO until appose new release cmd.addAll( INSTALL_PIP_DEPS );
+		cmd.addAll( INSTALL_EVSAM_PIP_DEPS );
+		final ProcessBuilder builder = new ProcessBuilder().directory( envFile );
+		//builder.inheritIO();
+		if ( PlatformDetection.isWindows() )
+		{
+			final Map< String, String > envs = builder.environment();
+			final String envDir = envFile.getAbsolutePath();
+			envs.put( "Path", envDir + ";" + envs.get( "Path" ) );
+			envs.put( "Path", Paths.get( envDir, "Scripts" ).toString() + ";" + envs.get( "Path" ) );
+			envs.put( "Path", Paths.get( envDir, "Library" ).toString() + ";" + envs.get( "Path" ) );
+			envs.put( "Path", Paths.get( envDir, "Library", "Bin" ).toString() + ";" + envs.get( "Path" ) );
+		} else {
+			final Map< String, String > envs = builder.environment();
+			final String envDir = envFile.getAbsolutePath();
+			envs.put( "PATH", envDir + ":" + envs.get( "PATH" ) );
+			envs.put( "PATH", Paths.get( envDir, "bin" ).toString() + ":" + envs.get( "PATH" ) );
+		}
+		if ( builder.command( cmd ).start().waitFor() != 0 )
+			throw new RuntimeException();
+	}
+
+	/**
+	 * TODO keep until release of stable Appose
+	 * Install the Python package to run Appose in Python
+	 * @param envName
+	 * 	environment where Appose is going to be installed
+	 * @throws IOException if there is any file creation related issue
+	 * @throws InterruptedException if the package installation is interrupted
+	 * @throws MambaInstallException if there is any error with the Mamba installation
+	 */
+	private void installApposePackage(String envName) throws IOException, InterruptedException, MambaInstallException {
+		installApposePackage(envName, false);
+	}
+
+	/**
+	 * TODO keep until release of stable Appose
+	 * Install the Python package to run Appose in Python
+	 * @param envName
+	 * 	environment where Appose is going to be installed
+	 * @param force
+	 * 	if the package already exists, whether to overwrite it or not
+	 * @throws IOException if there is any file creation related issue
+	 * @throws InterruptedException if the package installation is interrupted
+	 * @throws MambaInstallException if there is any error with the Mamba installation
+	 */
+	private void installApposePackage(String envName, boolean force) throws IOException, InterruptedException, MambaInstallException {
+		if (!checkMambaInstalled())
+			throw new IllegalArgumentException("Unable to SAM without first installing Mamba. ");
+		Thread thread = reportProgress(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- INSTALLING 'APPOSE' PYTHON PACKAGE");
+		String zipResourcePath = "appose-python.zip";
+        String outputDirectory = mamba.getEnvsDir() + File.separator + envName;
+        try (
+            	InputStream zipInputStream = SamEnvManagerAbstract.class.getClassLoader().getResourceAsStream(zipResourcePath);
+            	ZipInputStream zipInput = new ZipInputStream(zipInputStream);
+            		) {
+            	ZipEntry entry;
+            	while ((entry = zipInput.getNextEntry()) != null) {
+                    File entryFile = new File(outputDirectory + File.separator + entry.getName());
+                    if (entry.isDirectory()) {
+                    	entryFile.mkdirs();
+                    	continue;
+                    }
+                	entryFile.getParentFile().mkdirs();
+                    try (OutputStream entryOutput = new FileOutputStream(entryFile)) {
+                        byte[] buffer = new byte[1024];
+                        int bytesRead;
+                        while ((bytesRead = zipInput.read(buffer)) != -1) {
+                            entryOutput.write(buffer, 0, bytesRead);
+                        }
+                    }
+                }
+            } catch (IOException e) {
+    			thread.interrupt();
+    			passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- FAILED 'APPOSE' PYTHON PACKAGE INSTALLATION");
+    			throw e;
+    		}
+        mamba.pipInstallIn(envName, new String[] {mamba.getEnvsDir() + File.separator + envName + File.separator + APPOSE});
+		thread.interrupt();
+		passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- 'APPOSE' PYTHON PACKAGE INSATLLED");
+	}
+
+	/**
+	 * Method to install automatically Micromamba in the path of the corresponding {@link SamEnvManagerAbstract} instance.
+	 * 
+	 * @throws IOException if there is any file related error during the installation
+	 * @throws InterruptedException if the installation is interrupted
+	 * @throws ArchiveException if there is any error decompressing the micromamba installer files
+	 * @throws URISyntaxException if there is any error with the url that points to the micromamba instance to download
+	 * @throws MambaInstallException if there is any error installing micromamba
+	 */
+	public void installMambaPython() throws IOException, InterruptedException, 
+	ArchiveException, URISyntaxException, MambaInstallException{
+		if (checkMambaInstalled()) return;
+		Thread thread = reportProgress(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- INSTALLING MICROMAMBA");
+		try {
+			mamba.installMicromamba();
+		} catch (IOException | InterruptedException | ArchiveException | URISyntaxException e) {
+			thread.interrupt();
+			passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- FAILED MICROMAMBA INSTALLATION");
+			throw e;
+		}
+		thread.interrupt();
+		passToConsumer(LocalDateTime.now().format(DATE_FORMAT).toString() + " -- MICROMAMBA INSTALLED");
+	}
+
+	/**
+	 * 
+	 * @return the path to the folder where all the SAMJ environments are created
+	 */
+	public String getEnvsPath() {
+		return Paths.get(path, "envs").toFile().getAbsolutePath();
+	}
+
+	/**
+	 * Method that downloads a file
+	 * @param downloadURL
+	 * 	url of the file to be downloaded
+	 * @param targetFile
+	 * 	file where the file from the url will be downloaded too
+	 * @throws IOException if there si any error downloading the file
+	 * @throws URISyntaxException if there is any error in the URL syntax
+	 * @throws InterruptedException if the parent thread is stopped and the download stopped
+	 */
+	public void downloadFile(String downloadURL, File targetFile, Thread parentThread) 
+								throws IOException, URISyntaxException, InterruptedException {
+		FileOutputStream fos = null;
+		ReadableByteChannel rbc = null;
+		try {
+			URL website = new URL(downloadURL);
+	        HttpURLConnection conn = (HttpURLConnection) website.openConnection();
+	        conn.setRequestMethod("GET");
+	        conn.setRequestProperty("User-Agent", CommonUtils.getJDLLUserAgent());//"jdll/0.5.6 (Linux; Java 1.8.0_292)");
+	        rbc = Channels.newChannel(conn.getInputStream());
+			// TODO rbc = Channels.newChannel(website.openStream());
+			// Create the new model file as a zip
+			fos = new FileOutputStream(targetFile);
+			// Send the correct parameters to the progress screen
+			FileDownloader downloader = new FileDownloader(rbc, fos);
+			downloader.call(parentThread);
+		} finally {
+			if (fos != null)
+				fos.close();
+			if (rbc != null)
+				rbc.close();
+		}
+	}
+
+	/**
+	 * For a fresh, installation, SAMJ might need to download first micromamba. In that case, this method
+	 * returns the progress made for its download.
+	 * @return progress made downloading Micromamba
+	 */
+	public double getMambaInstallationProcess() {
+		return this.mamba.getMicromambaDownloadProgress();
+	}
+
+	public String getEnvCreationProgress() {
+		return this.getEnvCreationProgress();
+	}
+
+	private Thread reportProgress(String startStr) {
+		Thread currentThread = Thread.currentThread();
+		Thread thread = new Thread (() -> {
+			passToConsumer(startStr);
+			while (currentThread.isAlive()) {
+				try {Thread.sleep(300);} catch (InterruptedException e) {break;}
+				if (System.currentTimeMillis() - millis > 300)
+					passToConsumer("");
+			}
+		});
+		thread.start();
+		return thread;
+	}
+}