Merge pull request #896 from petebankhead/bf-fixes

Fix image selector/Bio-Formats bug

CHANGELOG.md

@@ -1,3 +1,11 @@
+## Version 0.4.0-SNAPSHOT
+
+This is a work-in-progress.
+
+### Bugs fixed
+* Reading from Bio-Formats blocks forever when using multiple series outside a project (https://github.com/qupath/qupath/issues/894)
+
+
 ## Version 0.3.2
 
 This is a *minor release* that aims to be fully compatible with v0.3.0 and v0.3.1 while fixing bugs.

qupath-extension-bioformats/src/main/java/qupath/lib/images/servers/bioformats/BioFormatsImageServer.java

@@ -272,7 +272,7 @@ static BioFormatsImageServer checkSupport(URI uri, final BioFormatsServerOptions
 
 	BioFormatsImageServer(URI uri, final BioFormatsServerOptions options, String...args) throws FormatException, IOException, DependencyException, ServiceException, URISyntaxException {
 		super();
-		
+
 		long startTime = System.currentTimeMillis();
 
 //		this.options = options;
@@ -1035,7 +1035,7 @@ private void createAdditionalReader(BioFormatsServerOptions options, final Class
 				if (isClosed)
 					return;
 				logger.debug("Requesting new reader for thread {}", Thread.currentThread());
-				var newReader = createReader(options, classList, id, new DummyMetadata(), args);
+				var newReader = createReader(options, classList, id, null, args);
 				if (newReader != null) {
 					additionalReaders.add(newReader);
 					queue.add(newReader);
@@ -1060,7 +1060,7 @@ private int getMaxReaders() {
 		 * @param options 	options used to control the reader generation
 		 * @param classList optionally specify a list of potential reader classes, if known (to avoid a more lengthy search)
 		 * @param id 		file path for the image.
-		 * @param store 	optional MetadataStore; this will be set in the reader if needed.
+		 * @param store 	optional MetadataStore; this will be set in the reader if needed. If it is unspecified, a dummy store will be created a minimal metadata requested.
 		 * @param args      optional args to customize reading
 		 * @return the {@code IFormatReader}
 		 * @throws FormatException
@@ -1122,11 +1122,12 @@ private IFormatReader createReader(final BioFormatsServerOptions options, final
 			}
 
 
-			if (store != null) {
+			if (store != null)
 				imageReader.setMetadataStore(store);
-			}
-			else
+			else {
 				imageReader.setMetadataStore(new DummyMetadata());
+				imageReader.setOriginalMetadataPopulated(false);
+			}
 
 			var swapDimensions = args.getSwapDimensions();
 			if (swapDimensions != null)
@@ -1200,7 +1201,14 @@ private IFormatReader nextQueuedReader() throws InterruptedException {
 					task = ForkJoinPool.commonPool().submit(() -> createAdditionalReader(options, classList, id, args));				
 				}
 			}
-			return queue.take();
+			if (isClosed)
+				return null;
+			try {
+				return queue.poll(60, TimeUnit.SECONDS);
+			} catch (InterruptedException e) {
+				logger.warn("Interrupted exception when awaiting next queued reader: {}", e.getLocalizedMessage());
+				return isClosed ? null : mainReader;
+			}
 		}
 
 
@@ -1415,10 +1423,9 @@ public void close() throws Exception {
 					logger.debug(e.getLocalizedMessage(), e);
 				}
 			}
-//			mainReader.close();
-//			for (var r : additionalReaders)
-//				r.close();
-			queue.clear();
+			// Allow the queue to be garbage collected - clearing could result in a queue.poll()
+			// lingering far too long
+//			queue.clear();
 		}
 
 

qupath-gui-fx/src/main/java/qupath/lib/gui/ServerSelector.java

@@ -180,6 +180,9 @@ public ImageServer<BufferedImage> promptToSelectServer() {
 
 
 		Dialog<ButtonType> dialog = new Dialog<>();
+		var qupath = QuPathGUI.getInstance();
+		if (qupath != null)
+			dialog.initOwner(qupath.getStage());
 		dialog.setTitle("Open image");
 		ButtonType typeImport = new ButtonType("Open", ButtonData.OK_DONE);
 		dialog.getDialogPane().getButtonTypes().addAll(typeImport, ButtonType.CANCEL);
@@ -208,24 +211,28 @@ public void handle(MouseEvent click) {
 
 		Optional<ButtonType> result = dialog.showAndWait();
 
+		var selectedToReturn = listSeries.getSelectionModel().getSelectedItem();
+
 		try {
 			executor.shutdownNow();
 		} catch (Exception e) {
 			logger.warn(e.getLocalizedMessage(), e);
 		} finally {
-			selectedSeries = null;
 			try {
-				for (ImageServer<BufferedImage> server: serverList)
-					server.close();
+				for (ImageServer<BufferedImage> server: serverList) {
+					if (server != selectedToReturn)
+						server.close();
+				}
 			} catch (Exception e) {
 				logger.debug(e.getLocalizedMessage(), e);
 			}
+			selectedSeries = null;
 		}		
 
 		if (!result.isPresent() || result.get() != typeImport || result.get() == ButtonType.CANCEL)
 			return null;
 
-		return listSeries.getSelectionModel().getSelectedItem();
+		return selectedToReturn;
 	}