add missing tool classes

src/main/java/ai/nets/samj/gui/components/ComboBoxItem.java

@@ -0,0 +1,100 @@
+/*-
+ * #%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.gui.components;
+
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+/**
+ * Class that allows identifying the objects in the list of a ComboBox by a unique identifier.
+ * This class helps associating a unique identifier to objects specific to a software.
+ * This class needs to be implemented on each software to be able to handle the native structures for images
+ * from the particualr software.
+ * @author CArlos Garcia
+ */
+public abstract class ComboBoxItem {
+    final private int id;
+    final private Object value;
+    private static final String SELECT_IMAGE_STR = "Select image";
+
+    /**
+     * An object that associates a unique identifier with an Object.
+     * The unique identifier cannot be -1, as it is reserved for empty objects
+     * @param uniqueID
+     * 	the unique identifier
+     * @param seq
+     * 	the object
+     */
+    public ComboBoxItem(int uniqueID, Object seq) {
+    	if (uniqueID == -1) throw new IllegalArgumentException("The unique identifier cannot be -1.");
+        this.id = uniqueID;
+        this.value = seq;
+    }
+
+    /**
+     * An object that associates a unique identifier with an Object.
+     * In this case it is empty, the unique identifier will by -1.
+     */
+    public ComboBoxItem() {
+        this.id = -1;
+        this.value = null;
+    }
+
+    /**
+     * 
+     * @return the unique identifier of the instance
+     */
+    public int getId() {
+        return id;
+    }
+
+    /**
+     * 
+     * @return the Object of interest
+     */
+    public Object getValue() {
+        return value;
+    }
+
+    /**
+     * 
+     * @return the name of the image. The way to retrieve the image (Object) name depends on the software where this is used,
+     * 	so it needs to be implemented on the software side
+     */
+    public abstract String getImageName();
+
+    /**
+     * Convert the software specific image into an ImgLib2 {@link RandomAccessibleInterval}
+     * @param <T>
+     * 	the possible ImgLib2 data types of the {@link RandomAccessibleInterval}
+     * @return the {@link RandomAccessibleInterval} created from the software image object
+     */
+    public abstract < T extends RealType< T > & NativeType< T > > RandomAccessibleInterval<T> getImageAsImgLib2();
+
+    @Override
+    /**
+     * {@inheritDoc}
+     */
+    public String toString() {
+    	if (value == null) return SELECT_IMAGE_STR;
+        return getImageName();
+    }
+}

src/main/java/ai/nets/samj/gui/tools/Files.java

@@ -0,0 +1,118 @@
+/*-
+ * #%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.gui.tools;
+
+import java.io.File;
+
+import javax.swing.JFileChooser;
+import javax.swing.filechooser.FileSystemView;
+
+/**
+ * Class that contains helper methods to browse and get specific files in the {@link JFileChooser}
+ * graphical user interface
+ * @author Daniel Sage
+ */
+public class Files {
+
+	/**
+	 * 
+	 * @return a String with the full path of the directory from where the code is being executed
+	 */
+	public static String getWorkingDirectory() {
+		return System.getProperty("user.dir");
+	}
+
+	/**
+	 * 
+	 * @return the path to the home directory of the computer
+	 */
+	public static String getHomeDirectory() {
+		return FileSystemView.getFileSystemView().getHomeDirectory().getAbsolutePath() + File.separator;	
+	}
+
+	/**
+	 * 
+	 * @return String path to the desktop directory
+	 */
+	public static String getDesktopDirectory() {
+		return getHomeDirectory() + "Desktop" + File.separator;
+	}
+
+	/**
+	 * Method that returns a {@link File} if the path provided is a File or false otherwise
+	 * @param path
+	 * 	String path to the file of interest
+	 * @return a {@link File} object for the file of interest or null if it does not exist
+	 */
+	public static File browseFile(String path) {
+		JFileChooser fc = new JFileChooser(); 
+		fc.setFileSelectionMode(JFileChooser.FILES_ONLY);
+		File dir = new File(path);
+		if (dir.exists())
+			fc.setCurrentDirectory(dir);
+
+		int ret = fc.showOpenDialog(null); 
+		if (ret == JFileChooser.APPROVE_OPTION) {
+			File file = new File(fc.getSelectedFile().getAbsolutePath());
+			if (file.exists())
+				return file;
+		}
+		return null;
+	}
+
+	/**
+	 * Method that returns a {@link File} if the path provided is a directory or false otherwise
+	 * @param path
+	 * 	String path to the directory of interest
+	 * @return a {@link File} object for the directory of interest or null if it does not exist
+	 */
+	public static File browseDirectory(String path) {
+		JFileChooser fc = new JFileChooser(); 
+		fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+		File dir = new File(path);
+		if (dir.exists())
+			fc.setCurrentDirectory(dir);
+
+		int ret = fc.showOpenDialog(null); 
+		if (ret == JFileChooser.APPROVE_OPTION) {
+			File file = new File(fc.getSelectedFile().getAbsolutePath());
+			if (file.exists())
+				return file;
+		}
+		return null;
+	}
+	/**
+	 * Delete all the contents of  a directory
+	 * @param folder
+	 * 	the File which is going to be deleted
+	 */
+	public static void deleteFolder(File folder) {
+	    File[] files = folder.listFiles();
+	    if (files == null) {
+	    	folder.delete();
+	    	return;
+	    }
+        for(File f: files) {
+            if(f.isDirectory()) deleteFolder(f);
+            else f.delete();
+        }
+	    folder.delete();
+	}
+}

src/main/java/ai/nets/samj/gui/tools/Tools.java

@@ -0,0 +1,50 @@
+/*-
+ * #%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.gui.tools;
+
+import java.awt.Desktop;
+import java.net.URL;
+
+/**
+ * Class that contains helper tools for SAMJ
+ * @author Daniel Sage
+ * @author Carlos Garcia
+ */
+public class Tools {
+
+	/**
+	 * Method that opens a website where there is some documentation about SAMJ
+	 * @return true if the method was able to access the website or false otherwise
+	 */
+	static public boolean help() {
+		String url = "https://github.com/segment-anything-models-java/SAMJ-IJ"; 
+		Desktop desktop = Desktop.isDesktopSupported() ? Desktop.getDesktop() : null;
+		if (desktop != null && desktop.isSupported(Desktop.Action.BROWSE)) {
+			try {
+				desktop.browse(new URL(url).toURI());
+				return true;
+			}
+			catch (Exception e) {
+				e.printStackTrace();
+			}
+		}
+		return false;
+	}
+}