use methods from GeneralTools for getting filename (#1483)

1. delete `Utils.getFileName` and `Utils.getNameWithoutExtension`
2. get filename by `GeneralTools.toPath` from URIs.
3. get file extension by `GeneralTools.getExtension(File)`

this fix #1480

Signed-off-by: Butui Hu <[email protected]>
Co-authored-by: SACHIDANAND ALLE <[email protected]>

Author: hubutui

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/InteractorTool.java

@@ -7,6 +7,7 @@
 import org.slf4j.LoggerFactory;
 
 import javafx.scene.input.MouseEvent;
+import qupath.lib.common.GeneralTools;
 import qupath.lib.extension.monailabel.MonaiLabelClient.ResponseInfo;
 import qupath.lib.extension.monailabel.commands.RunInference;
 import qupath.lib.gui.dialogs.Dialogs;
@@ -59,9 +60,10 @@ public void mousePressed(MouseEvent e) {
 				model = names.get(0);
 			}
 
-			String imageFile = Utils.getFileName(viewer.getImageData().getServerPath());
-			String im = imageFile.toLowerCase();
-			boolean isWSI = (im.endsWith(".png") || im.endsWith(".jpg") || im.endsWith(".jpeg")) ? false : true;
+			var uris = viewer.getImageData().getServer().getURIs();
+			String imageFile = GeneralTools.toPath(uris.iterator().next()).toString();
+			String ext = GeneralTools.getExtension(imageFile).get().toLowerCase();
+			boolean isWSI = !(ext.equals(".png") || ext.equals(".jpg") || ext.equals(".png"));
 			logger.info("MONAILabel:: isWSI: " + isWSI + "; File: " + imageFile);
 
 			if (model == null || model.isEmpty()) {

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/SegmentationTool.java

@@ -7,6 +7,7 @@
 import org.slf4j.LoggerFactory;
 
 import javafx.scene.input.MouseEvent;
+import qupath.lib.common.GeneralTools;
 import qupath.lib.extension.monailabel.MonaiLabelClient.ResponseInfo;
 import qupath.lib.extension.monailabel.commands.RunInference;
 import qupath.lib.gui.dialogs.Dialogs;
@@ -40,9 +41,10 @@ public void mouseReleased(MouseEvent e) {
 			return;
 
 		try {
-			String imageFile = Utils.getFileName(viewer.getImageData().getServerPath());
-			String im = imageFile.toLowerCase();
-			boolean isWSI = (im.endsWith(".png") || im.endsWith(".jpg") || im.endsWith(".jpeg")) ? false : true;
+			var uris = viewer.getImageData().getServer().getURIs();
+			String imageFile = GeneralTools.toPath(uris.iterator().next()).toString();
+			String ext = GeneralTools.getExtension(imageFile).get().toLowerCase();
+			boolean isWSI = !(ext.equals(".png") || ext.equals(".jpg") || ext.equals(".png"));
 			logger.info("MONAILabel:: isWSI: " + isWSI + "; File: " + imageFile);
 
 			if (info == null) {

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/Utils.java

@@ -13,7 +13,6 @@
 
 package qupath.lib.extension.monailabel;
 
-import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -25,21 +24,6 @@
 
 public class Utils {
 
-	public static String getFileName(String file) {
-		if (file.indexOf("file:/") >= 0)
-			file = file.substring(file.indexOf("file:/") + "file:/".length());
-
-		int pos = file.indexOf("[");
-		file = file.substring(0, pos > 0 ? pos : file.length());
-		return file;
-	}
-
-	public static String getNameWithoutExtension(String file) {
-		String fileName = new File(file).getName();
-		int dotIndex = fileName.lastIndexOf('.');
-		return (dotIndex == -1) ? fileName : fileName.substring(0, dotIndex);
-	}
-
 	public static int[] getBBOX(ROI roi) {
 		int x = 0, y = 0, w = 0, h = 0;
 		if (roi != null && roi instanceof RectangleROI) {

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/commands/NextSample.java

@@ -21,6 +21,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import qupath.lib.common.GeneralTools;
 import qupath.lib.extension.monailabel.MonaiLabelClient;
 import qupath.lib.extension.monailabel.MonaiLabelClient.NextSampleInfo;
 import qupath.lib.extension.monailabel.MonaiLabelClient.ResponseInfo;
@@ -50,7 +51,12 @@ public void run() {
 		try {
 			var viewer = qupath.getViewer();
 			var imageData = viewer.getImageData();
-			String image = imageData != null ? Utils.getNameWithoutExtension(imageData.getServerPath()) : "";
+			String image = "";
+			if (imageData != null) {
+				var uris = imageData.getServer().getURIs();
+				File imageFile = GeneralTools.toPath(uris.iterator().next()).toFile();
+				image = GeneralTools.getNameWithoutExtension(imageFile);
+			}
 
 			ResponseInfo info = MonaiLabelClient.info();
 			List<String> names = new ArrayList<String>();

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/commands/RunInference.java

@@ -35,6 +35,7 @@
 import org.xml.sax.SAXException;
 
 import javafx.concurrent.Task;
+import qupath.lib.common.GeneralTools;
 import qupath.lib.extension.monailabel.MonaiLabelClient;
 import qupath.lib.extension.monailabel.MonaiLabelClient.RequestInfer;
 import qupath.lib.extension.monailabel.MonaiLabelClient.ResponseInfo;
@@ -84,9 +85,10 @@ public void run() {
 				return;
 			}
 
-			String imageFile = Utils.getFileName(viewer.getImageData().getServerPath());
-			String im = imageFile.toLowerCase();
-			boolean isWSI = !im.endsWith(".png") && !im.endsWith(".jpg") && !im.endsWith(".jpeg");
+			var uris = imageData.getServer().getURIs();
+			String imageFile = GeneralTools.toPath(uris.iterator().next()).toString();
+			String ext = GeneralTools.getExtension(imageFile).get().toLowerCase();
+			boolean isWSI = !(ext.equals(".png") || ext.equals(".jpg") || ext.equals(".png"));
 			logger.info("MONAILabel:: isWSI: " + isWSI + "; File: " + imageFile);
 
 			// Select first RectangleROI if not selected explicitly
@@ -230,7 +232,7 @@ public static void runInference(String model, ResponseInfo info, int[] bbox, int
 
 			ROI roi = ROIs.createRectangleROI(bbox[0], bbox[1], bbox[2], bbox[3], null);
 
-			String image = Utils.getNameWithoutExtension(imageFile);
+			String image = GeneralTools.getNameWithoutExtension(new File(imageFile));
 			String sessionId = null;
 			int offsetX = 0;
 			int offsetY = 0;

plugins/qupath/src/main/java/qupath/lib/extension/monailabel/commands/SubmitLabel.java

@@ -37,6 +37,7 @@
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
+import qupath.lib.common.GeneralTools;
 import qupath.lib.extension.monailabel.MonaiLabelClient;
 import qupath.lib.extension.monailabel.MonaiLabelClient.ImageInfo;
 import qupath.lib.extension.monailabel.Utils;
@@ -67,11 +68,11 @@ public void run() {
 		try {
 			var viewer = qupath.getViewer();
 			var imageData = viewer.getImageData();
-			String imageFile = Utils.getFileName(imageData.getServerPath());
-			String image = Utils.getNameWithoutExtension(imageFile);
-
-			String im = imageFile.toLowerCase();
-			boolean isWSI = (im.endsWith(".png") || im.endsWith(".jpg") || im.endsWith(".jpeg")) ? false : true;
+			var uris = imageData.getServer().getURIs();
+			String imageFile = GeneralTools.toPath(uris.iterator().next()).toString();
+			String image = GeneralTools.getNameWithoutExtension(new File(imageFile));
+			String ext = GeneralTools.getExtension(imageFile).get().toLowerCase();
+			boolean isWSI = !(ext.equals(".png") || ext.equals(".jpg") || ext.equals(".png"));
 			logger.info("MONAILabel:: isWSI: " + isWSI + "; File: " + imageFile);
 
 			boolean validImage = MonaiLabelClient.imageExists(image);