Merge pull request qupath#1318 from petebankhead/detach-viewers

Make viewers 'detachable'

CHANGELOG.md

@@ -5,8 +5,6 @@ This is a work-in-progress for the next QuPath release.
 ### Enhancements
 * New toolbar buttons for script editor `</>` and log viewer
 * *File &rarr; Export snapshots* supports PNG, JPEG and TIFF (not just PNG)
-* New preference to control whether the 'system menubar' is used globally, or just for the main window
-   * Makes a difference on macOS, doesn't on Windows... on Linux it depends
 
 ### Bugs fixed
 * Rendered image export does not support opacity (https://github.com/qupath/qupath/issues/1292)
@@ -19,6 +17,7 @@ This is a work-in-progress for the next QuPath release.
 * PathIO doesn't restore backup if writing ImageData fails (https://github.com/qupath/qupath/issues/1252)
 * Scripts open with the caret at the bottom of the text rather than the top (https://github.com/qupath/qupath/issues/1258)
 * 'Synchronize viewers' ignores z and t positions (https://github.com/qupath/qupath/issues/1220)
+* Menubars and shortcuts are confused when ImageJ is open but QuPath is in focus in macOS (https://github.com/qupath/qupath/issues/6)
 
 ### Dependency updates
 * Bio-Formats 7.0.0

qupath-core-processing/src/main/java/qupath/imagej/detect/cells/SubcellularDetection.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -92,9 +92,9 @@ public class SubcellularDetection extends AbstractInteractivePlugin<BufferedImag
 
 
 	@Override
-	public boolean runPlugin(final PluginRunner<BufferedImage> pluginRunner, final String arg) {
-		boolean success = super.runPlugin(pluginRunner, arg);
-		getHierarchy(pluginRunner).fireHierarchyChangedEvent(this);
+	public boolean runPlugin(final PluginRunner pluginRunner, final ImageData<BufferedImage> imageData, final String arg) {
+		boolean success = super.runPlugin(pluginRunner, imageData, arg);
+		imageData.getHierarchy().fireHierarchyChangedEvent(this);
 		return success;
 	}
 
@@ -441,10 +441,10 @@ public String getDescription() {
 	}
 
 	@Override
-	protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
+	protected Collection<PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
 		Collection<Class<? extends PathObject>> parentClasses = getSupportedParentObjectClasses();
 		List<PathObject> parents = new ArrayList<>();
-		for (PathObject parent : getHierarchy(runner).getSelectionModel().getSelectedObjects()) {
+		for (PathObject parent : imageData.getHierarchy().getSelectionModel().getSelectedObjects()) {
 			for (Class<? extends PathObject> cls : parentClasses) {
 				if (cls.isAssignableFrom(parent.getClass())) {
 					parents.add(parent);

qupath-core-processing/src/main/java/qupath/imagej/detect/dearray/TMADearrayerPluginIJ.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -55,7 +55,6 @@
 import qupath.lib.plugins.AbstractInteractivePlugin;
 import qupath.lib.plugins.ObjectDetector;
 import qupath.lib.plugins.PathPlugin;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.plugins.workflow.SimplePluginWorkflowStep;
 import qupath.lib.plugins.workflow.WorkflowStep;
@@ -377,8 +376,8 @@ public String getDescription() {
 
 
 	@Override
-	protected Collection<? extends PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		return Collections.singletonList(runner.getImageData().getHierarchy().getRootObject());
+	protected Collection<? extends PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		return Collections.singletonList(imageData.getHierarchy().getRootObject());
 	}
 
 

qupath-core-processing/src/main/java/qupath/imagej/detect/tissue/SimpleTissueDetection2.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -63,7 +63,6 @@
 import qupath.lib.plugins.AbstractDetectionPlugin;
 import qupath.lib.plugins.DetectionPluginTools;
 import qupath.lib.plugins.ObjectDetector;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.ImagePlane;
 import qupath.lib.regions.RegionRequest;
@@ -442,9 +441,9 @@ protected void addRunnableTasks(ImageData<BufferedImage> imageData, PathObject p
 
 
 	@Override
-	protected Collection<? extends PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
+	protected Collection<? extends PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
 
-		PathObjectHierarchy hierarchy = getHierarchy(runner);
+		PathObjectHierarchy hierarchy = imageData.getHierarchy();
 		if (hierarchy.getTMAGrid() == null)
 			return Collections.singleton(hierarchy.getRootObject());
 

qupath-core-processing/src/main/java/qupath/imagej/superpixels/DoGSuperpixelsPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -52,7 +52,6 @@
 import qupath.lib.objects.PathObjects;
 import qupath.lib.plugins.AbstractTileableDetectionPlugin;
 import qupath.lib.plugins.ObjectDetector;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.RegionRequest;
 import qupath.lib.roi.RoiTools;
@@ -269,8 +268,8 @@ public String getDescription() {
 
 
 	@Override
-	protected synchronized Collection<? extends PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		Collection<? extends PathObject> parents = super.getParentObjects(runner);
+	protected synchronized Collection<? extends PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		Collection<? extends PathObject> parents = super.getParentObjects(imageData);
 		return parents;
 
 		// Exploring the use of hidden objects...

qupath-core-processing/src/main/java/qupath/imagej/superpixels/SLICSuperpixelsPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -52,7 +52,6 @@
 import qupath.lib.objects.PathObjects;
 import qupath.lib.plugins.AbstractTileableDetectionPlugin;
 import qupath.lib.plugins.ObjectDetector;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.RegionRequest;
 import qupath.lib.roi.RoiTools;
@@ -549,8 +548,8 @@ public String getDescription() {
 
 
 	@Override
-	protected synchronized Collection<? extends PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		Collection<? extends PathObject> parents = super.getParentObjects(runner);
+	protected synchronized Collection<? extends PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		Collection<? extends PathObject> parents = super.getParentObjects(imageData);
 		return parents;
 	}
 

qupath-core-processing/src/main/java/qupath/lib/algorithms/CoherenceFeaturePlugin.java

@@ -352,8 +352,8 @@ public String getDescription() {
 	}
 
 	@Override
-	protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		return runner.getImageData().getHierarchy().getDetectionObjects();
+	protected Collection<PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		return imageData.getHierarchy().getDetectionObjects();
 	}
 
 	@Override

qupath-core-processing/src/main/java/qupath/lib/algorithms/HaralickFeaturesPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -57,7 +57,6 @@
 import qupath.lib.objects.PathObject;
 import qupath.lib.objects.TMACoreObject;
 import qupath.lib.plugins.AbstractInteractivePlugin;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.RegionRequest;
 import qupath.lib.roi.interfaces.ROI;
@@ -476,8 +475,8 @@ public String getDescription() {
 	}
 
 	@Override
-	protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		return runner.getImageData().getHierarchy().getSelectionModel().getSelectedObjects();
+	protected Collection<PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		return imageData.getHierarchy().getSelectionModel().getSelectedObjects();
 //		return runner.getImageData().getHierarchy().getSelectionModel().getSelectedObjects();
 //		return runner.getImageData().getHierarchy().getObjects(null, PathDetectionObject.class);
 	}

qupath-core-processing/src/main/java/qupath/lib/algorithms/IntensityFeaturesPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -351,9 +351,9 @@ public float[] getTransformedPixels(final BufferedImage img, int[] buf, final Co
 
 
 	@Override
-	public boolean runPlugin(final PluginRunner<BufferedImage> pluginRunner, final String arg) {
-		boolean success = super.runPlugin(pluginRunner, arg);
-		getHierarchy(pluginRunner).fireHierarchyChangedEvent(this);
+	public boolean runPlugin(final PluginRunner pluginRunner, final ImageData<BufferedImage> imageData, final String arg) {
+		boolean success = super.runPlugin(pluginRunner, imageData, arg);
+		imageData.getHierarchy().fireHierarchyChangedEvent(this);
 		return success;
 	}
 
@@ -716,8 +716,8 @@ public String getDescription() {
 	}
 
 	@Override
-	protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		return runner.getImageData().getHierarchy().getSelectionModel().getSelectedObjects();
+	protected Collection<PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		return imageData.getHierarchy().getSelectionModel().getSelectedObjects();
 	}
 
 	@Override

qupath-core-processing/src/main/java/qupath/lib/algorithms/LocalBinaryPatternsPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -50,7 +50,6 @@
 import qupath.lib.objects.PathDetectionObject;
 import qupath.lib.objects.PathObject;
 import qupath.lib.plugins.AbstractInteractivePlugin;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.RegionRequest;
 import qupath.lib.roi.interfaces.ROI;
@@ -310,8 +309,8 @@ public String getDescription() {
 	}
 
 	@Override
-	protected Collection<PathObject> getParentObjects(final PluginRunner<BufferedImage> runner) {
-		return runner.getImageData().getHierarchy().getDetectionObjects();
+	protected Collection<PathObject> getParentObjects(final ImageData<BufferedImage> imageData) {
+		return imageData.getHierarchy().getDetectionObjects();
 	}
 
 	@Override

qupath-core-processing/src/main/java/qupath/lib/plugins/objects/DilateAnnotationPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -44,7 +44,6 @@
 import qupath.lib.objects.PathObjects;
 import qupath.lib.objects.hierarchy.PathObjectHierarchy;
 import qupath.lib.plugins.AbstractInteractivePlugin;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.regions.ImagePlane;
 import qupath.lib.roi.GeometryTools;
@@ -135,24 +134,24 @@ public ParameterList getDefaultParameterList(ImageData<T> imageData) {
 	}
 
 	@Override
-	protected Collection<? extends PathObject> getParentObjects(PluginRunner<T> runner) {
-		return getHierarchy(runner).getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation()).toList();
+	protected Collection<? extends PathObject> getParentObjects(ImageData<T> imageData) {
+		return imageData.getHierarchy().getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation()).toList();
 	}
 
 	@Override
 	protected void addRunnableTasks(ImageData<T> imageData, PathObject parentObject, List<Runnable> tasks) {}
 
 	@Override
-	protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
-		Collection<? extends PathObject> parentObjects = getParentObjects(runner);
+	protected Collection<Runnable> getTasks(final ImageData<T> imageData) {
+		Collection<? extends PathObject> parentObjects = getParentObjects(imageData);
 		if (parentObjects == null || parentObjects.isEmpty())
 			return Collections.emptyList();
 
 		// Add a single task, to avoid multithreading - which may complicate setting parents
 		List<Runnable> tasks = new ArrayList<>(parentObjects.size());
-		ImageServer<T> server = getServer(runner);
+		ImageServer<T> server = imageData.getServer();
 		Rectangle bounds = new Rectangle(0, 0, server.getWidth(), server.getHeight());
-		PathObjectHierarchy hierarchy = getHierarchy(runner);
+		PathObjectHierarchy hierarchy = imageData.getHierarchy();
 
 		double radiusPixels;
 		PixelCalibration cal = server.getPixelCalibration();

qupath-core-processing/src/main/java/qupath/lib/plugins/objects/FillAnnotationHolesPlugin.java

@@ -35,7 +35,6 @@
 import qupath.lib.objects.PathROIObject;
 import qupath.lib.objects.hierarchy.PathObjectHierarchy;
 import qupath.lib.plugins.AbstractInteractivePlugin;
-import qupath.lib.plugins.PluginRunner;
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.roi.RoiTools;
 import qupath.lib.roi.interfaces.ROI;
@@ -80,22 +79,22 @@ public ParameterList getDefaultParameterList(ImageData<T> imageData) {
 	}
 
 	@Override
-	protected Collection<? extends PathObject> getParentObjects(PluginRunner<T> runner) {
-		return getHierarchy(runner).getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation()).toList();
+	protected Collection<? extends PathObject> getParentObjects(ImageData<T> imageData) {
+		return imageData.getHierarchy().getSelectionModel().getSelectedObjects().stream().filter(p -> p.isAnnotation()).toList();
 	}
 
 	@Override
 	protected void addRunnableTasks(ImageData<T> imageData, PathObject parentObject, List<Runnable> tasks) {}
 
 	@Override
-	protected Collection<Runnable> getTasks(final PluginRunner<T> runner) {
-		Collection<? extends PathObject> parentObjects = getParentObjects(runner);
+	protected Collection<Runnable> getTasks(final ImageData<T> imageData) {
+		Collection<? extends PathObject> parentObjects = getParentObjects(imageData);
 		if (parentObjects == null || parentObjects.isEmpty())
 			return Collections.emptyList();
 
 		// Add a single task, to avoid multithreading - which may complicate setting parents
 		List<Runnable> tasks = new ArrayList<>(1);
-		PathObjectHierarchy hierarchy = getHierarchy(runner);
+		PathObjectHierarchy hierarchy = imageData.getHierarchy();
 
 		// Want to reset selection
 		PathObject selected = hierarchy.getSelectionModel().getSelectedObject();

qupath-core-processing/src/main/java/qupath/lib/plugins/objects/FindConvexHullDetectionsPlugin.java

@@ -4,7 +4,7 @@
  * %%
  * Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
  * Contact: IP Management (ipmanagement@qub.ac.uk)
- * Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
+ * Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh
  * %%
  * QuPath is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as
@@ -113,8 +113,8 @@ public String getLastResultsDescription() {
 	}
 
 	@Override
-	protected Collection<? extends PathObject> getParentObjects(PluginRunner<T> runner) {
-		PathObjectHierarchy hierarchy = getHierarchy(runner);
+	protected Collection<? extends PathObject> getParentObjects(ImageData<T> imageData) {
+		PathObjectHierarchy hierarchy = imageData.getHierarchy();
 		PathObject selected = hierarchy.getSelectionModel().getSelectedObject();
 		if (selected instanceof TMACoreObject)
 			return Collections.singleton(selected);
@@ -138,9 +138,9 @@ public ParameterList getDefaultParameterList(ImageData<T> imageData) {
 
 
 	@Override
-	public boolean runPlugin(final PluginRunner<T> pluginRunner, final String arg) {
+	public boolean runPlugin(final PluginRunner pluginRunner, final ImageData<T> imageData, final String arg) {
 		nObjectsRemoved.set(0);
-		return super.runPlugin(pluginRunner, arg);
+		return super.runPlugin(pluginRunner, imageData, arg);
 	}