Update to build

Access the BasicStitching plugin through maven local.

build.gradle

@@ -42,8 +42,9 @@ dependencies {
     shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
     //Access to BioFormats extension for writing ome.tif files
     implementation "io.github.qupath:qupath-extension-bioformats:${qupathVersion}"
+    //implementation "qupath.ext.basicstitching:BasicStitching:${qupathVersion}"
+
     //TODO figure out syntax for other plugins
-    //implementation "io.github.qupath:BasicStitchingExtension:${qupathVersion}"
     // For logging - the version comes from QuPath's version catalog at
     // https://github.com/qupath/qupath/blob/main/gradle/libs.versions.toml
     // See https://docs.gradle.org/current/userguide/platforms.html
@@ -138,17 +139,16 @@ tasks.named('test') {
 // within QuPath itself (which is useful during development).
 repositories {
     // Add this if you need access to dependencies only installed locally
-    //  mavenLocal()
-
+    mavenLocal()
+    /*
+    flatDir{
+        dirs 'C:/ImageAnalysis/QPExtensionTest/BasicStitching/build/libs'
+    }
+    */
     mavenCentral()
 
     // Add scijava - which is where QuPath's jars are hosted
     maven {
-        url "https://maven.scijava.org/content/repositories/releases"
-    }
-
-    maven {
-        url "https://maven.scijava.org/content/repositories/snapshots"
+        url "https://maven.scijava.org/content/groups/public"
     }
-
-}
+}

src/main/groovy/qupath/ext/qp_scope/QP_scope.groovy

@@ -5,15 +5,10 @@ import qupath.lib.common.Version;
 import qupath.lib.gui.QuPathGUI
 import qupath.lib.gui.extensions.QuPathExtension;
 import qupath.ext.qp_scope.functions.*
+import org.slf4j.LoggerFactory
 
 /**
- * This is a demo to provide a template for creating a new QuPath extension in Groovy.
- * <p>
- * <b>Important!</b> For your extension to work in QuPath, you need to make sure the name & package
- * of this class is consistent with the file
- * <pre>
- *     /resources/META-INF/services/qupath.lib.gui.extensions.QuPathExtension
- * </pre>
+ * Built from the QuPath extension template - an extension to control a microscope through a Python interface
  */
 class QP_scope implements QuPathExtension {
 
@@ -53,9 +48,15 @@ class QP_scope implements QuPathExtension {
 	}
 
 	private void addMenuItem(QuPathGUI qupath) {
+		def logger = LoggerFactory.getLogger(QuPathGUI.class)
+		//Check for dependencies and QuPath version
+		logger.info("QuPath Version")
+		logger.info(getQuPathVersion().toString())
+		//TODO how to check if version is supported?
+
 		def menu = qupath.getMenu("Extensions>${name}", true)
 		def fileNameStitching = new MenuItem("Start qp_scope")
-		// TODO tooltip "Coordinates are expected to be in the format ImageName[xCoordinateInMicrons, yCoordinateInMicrons].tif"
+		// TODO tooltip
 		fileNameStitching.setOnAction(e -> {
 			//TODO check preferences for all necessary entries
 

src/main/groovy/qupath/ext/qp_scope/functions/QP_scope_GUI.groovy

@@ -10,11 +10,14 @@ import javafx.stage.Modality
 import qupath.ext.qp_scope.utilities.utilityFunctions
 import qupath.lib.gui.dialogs.Dialogs
 import groovy.io.FileType
-import java.awt.image.BufferedImage
-import qupath.lib.images.servers.ImageServerProvider
+import qupath.lib.projects.Project
+import qupath.lib.gui.QuPathGUI
+import qupath.lib.scripting.QP
+import qupath.lib.gui.scripting.QPEx
+import qupath.ext.basicstitching.BasicStitchingExtension
 
 
-class QP_scope_GUI {
+public class QP_scope_GUI {
 
     // Existing text fields
     static TextField x1Field = new TextField("");
@@ -35,7 +38,7 @@ class QP_scope_GUI {
         def dlg = new Dialog<ButtonType>();
         dlg.initModality(Modality.APPLICATION_MODAL);
         dlg.setTitle("qp_scope");
-        dlg.setHeaderText("Enter details:");
+        dlg.setHeaderText("Enter details (LOOK MA! " + BasicStitchingExtension.class.getName() + "!):");
 
         // Set the content
         dlg.getDialogPane().setContent(createContent());
@@ -75,14 +78,28 @@ class QP_scope_GUI {
             if ([sampleLabel, x1, y1, x2, y2, virtualEnvPath, pythonScriptPath].any { it == null || it.isEmpty() }) {
                 Dialogs.showWarningNotification("Warning!", "Incomplete data entered.");
             } else {
-                Object project = utilityFunctions.createProjectFolder(projectsFolderPath,sampleLabel, preferences.firstScanType)
+                Project currentQuPathProject= utilityFunctions.createProjectFolder(projectsFolderPath, sampleLabel, preferences.firstScanType)
+
                 utilityFunctions.runPythonCommand(virtualEnvPath, pythonScriptPath, projectsFolderPath, sampleLabel, x1, y1, x2, y2);
 
                 //TODO figure out how to call stitching function in other plugin
+
                 utilityFunctions.showAlertDialog("Wait and complete stitching in other version of QuPath")
-                String stitchedImagePathStr = projectsFolderPath + File.separator + sampleLabel + File.separator + "SlideImages" + File.separator + preferences.firstScanType + sampleLabel;
+                String stitchedImagePathStr = projectsFolderPath + File.separator + sampleLabel + File.separator + "SlideImages" + File.separator + preferences.firstScanType + sampleLabel + ".ome.tif";
                 File stitchedImagePath = new File(stitchedImagePathStr);
-                utilityFunctions.addImageToProject(stitchedImagePath, project)
+                utilityFunctions.addImageToProject(stitchedImagePath, currentQuPathProject)
+
+                //open the newly created project
+                //https://qupath.github.io/javadoc/docs/qupath/lib/gui/QuPathGUI.html#setProject(qupath.lib.projects.Project)
+                def qupathGUI = QPEx.getQuPath()
+
+                qupathGUI.setProject(currentQuPathProject)
+                //Find the existing images - there should only be one since the project was just created
+                def firstImage = currentQuPathProject.getImageList()[0]
+
+                //Open the first image
+                //https://qupath.github.io/javadoc/docs/qupath/lib/gui/QuPathGUI.html#openImageEntry(qupath.lib.projects.ProjectImageEntry)
+                qupathGUI.openImageEntry(firstImage)
 
                 //}
             }
@@ -118,5 +135,4 @@ class QP_scope_GUI {
         pane.add(control, 1, rowIndex);
     }
 
-
 }

src/main/groovy/qupath/ext/qp_scope/utilities/utilityFunctions.groovy

@@ -2,8 +2,9 @@ package qupath.ext.qp_scope.utilities
 
 import org.slf4j.LoggerFactory
 import qupath.lib.gui.QuPathGUI
+import qupath.lib.gui.dialogs.Dialogs
 import qupath.lib.images.servers.ImageServerProvider
-
+import qupath.lib.projects.ProjectIO
 import java.awt.image.BufferedImage
 import qupath.lib.projects.Projects;
 import java.io.File
@@ -30,20 +31,26 @@ class utilityFunctions {
     }
 
     static boolean addImageToProject(File stitchedImagePath, Project project){
+        def logger = LoggerFactory.getLogger(QuPathGUI.class)
 
-        def imagePath = stitchedImagePath.getCanonicalPath()
+        def imagePath = stitchedImagePath.toURI().toString()
+        //logger.info(imagePath)
 
-        def support = ImageServerProvider.getPreferredUriImageSupport(BufferedImage.class, imagePath, "")
-        println(support)
+        def support = ImageServerProvider.getPreferredUriImageSupport(BufferedImage.class, imagePath)
+        //logger.info(support as String)
         def builder = support.builders.get(0)
         // Make sure we don't have null
         if (builder == null) {
-            print "Image not supported: " + imagePath
+            logger.warn("Image not supported: " + imagePath)
             return false
         }
 
         // Add the image as entry to the project
-        print "Adding: " + imagePath
+        logger.info("Adding: " + imagePath)
+        if (project == null) {
+            logger.warn("Project is null, there must have been a problem creating the project")
+            return false
+        }
         Object entry = project.addImage(builder)
 
         // Set a particular image type
@@ -63,6 +70,8 @@ class utilityFunctions {
 }
 
     static Project createProjectFolder(String projectsFolderPath, String sampleLabel, String scanType) {
+        //TODO check if a project is open! It probably should not be?
+
         // Ensure that the projectsFolderPath exists, if it does not, create it.
         File projectsFolder = new File(projectsFolderPath)
         if (!projectsFolder.exists()) {
@@ -76,15 +85,28 @@ class utilityFunctions {
         }
 
         // Check for a .qpproj file in the sampleLabel folder
-        File[] qpprojFiles = sampleLabelFolder.listFiles({ File f -> f.name.endsWith('.qpproj') } as FilenameFilter)
-        //Create a QuPath project in the sampleLabelFolder, within the projects folder
+        File[] qpprojFiles = sampleLabelFolder.listFiles({ dir, name -> name.endsWith('.qpproj') } as FilenameFilter)
+        //Create a QuPath project in the sampleLabelFolder, within the projects folder, provided there are no existing .qpproj files
         Project project = null
         if (qpprojFiles == null || qpprojFiles.length == 0) {
             project = Projects.createProject(sampleLabelFolder, BufferedImage.class)
+        }else{
+            //WARNING: This assumes there will be only one file ending in .qpproj
+            // this should USUALLY be a safe assumption
+            if (qpprojFiles.length > 1){
+                Dialogs.showWarningNotification("Warning!", "Multiple Project files found, may cause unexpected behavior!")
+            }
+
+            project = ProjectIO.loadProject(qpprojFiles[0], BufferedImage.class)
         }
 
+        if (project == null) {
+            Dialogs.showWarningNotification("Warning!", "Project is null!")
+        }
         // Within projectsFolderPath, check for a folder with the name "SlideImages", if it does not exist, create it
-        File slideImagesFolder = new File(projectsFolder, sampleLabelFolder, "SlideImages")
+        String slideImagesFolderPathStr = projectsFolderPath + File.separator + sampleLabel + File.separator + "SlideImages" ;
+        File slideImagesFolder =  new File(slideImagesFolderPathStr);
+
         if (!slideImagesFolder.exists()) {
             slideImagesFolder.mkdirs()
         }
@@ -94,6 +116,7 @@ class utilityFunctions {
         if (!scanTypeFolder.exists()) {
             scanTypeFolder.mkdirs()
         }
+
         return project
     }
 
@@ -143,6 +166,7 @@ class utilityFunctions {
         //TODO add code to access Preferences fields
         //If preferences are null or missing, throw an error and close
         //Open to discussion whether scan types should be included here or typed every time, or some other option
-        return [installation: "C:\\ImageAnalysis\\python", environment: "C:\\Anaconda\\envs\\paquo", projects: "C:\\ImageAnalysis\\slides", firstScanType: "4x_bf_", secondScanType:"20x_bf"]
+        //TODO fix the installation to be a folder with an expected .py file target? Or keep as .py file target?
+        return [installation: "C:\\ImageAnalysis\\python\\py_dummydoc.py", environment: "C:\\Anaconda\\envs\\paquo", projects: "C:\\ImageAnalysis\\slides", firstScanType: "4x_bf_", secondScanType:"20x_bf"]
     }
 }