Merge pull request #1241 from petebankhead/late-fixes

Fix memoization on Windows, directory prefs

CHANGELOG.md

@@ -1,4 +1,4 @@
-## Version 0.4.3-SNAPSHOT
+## Version 0.4.3
 
 This is a *minor release* that aims to be fully compatible with previous v0.4.x releases, while fixing bugs.
 
@@ -11,8 +11,10 @@ This is a *minor release* that aims to be fully compatible with previous v0.4.x
 ### Bugs fixed
 * Opening the same image in multiple viewers results in detections being wrongly shown in both (https://github.com/qupath/qupath/issues/1217)
 * 'Transform annotations' can't be applied to selected objects when double-clicking to end the transform (https://github.com/qupath/qupath/issues/1231)
-* Wrong script generated for 'Add intensity features' with some tile shapes (https://github.com/qupath/qupath/issues/1227)
+* Unusable script generated for 'Add intensity features' with some tile shapes (https://github.com/qupath/qupath/issues/1227)
+* Unusable generated for 'Expand annotations' with some line caps (https://github.com/qupath/qupath/issues/1227)
 * 'Tile classifications to annotations' is broken (https://github.com/qupath/qupath/issues/1226)
+* Directory preferences cannot be reset (https://github.com/qupath/qupath/issues/1240)
 
 ### Dependency updates
 * Bio-Formats 6.12.0

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

@@ -167,10 +167,10 @@ public class BioFormatsImageServer extends AbstractTileableImageServer {
 	private String[] args;
 
 	/**
-	 * Path to the base image file - will be the same as path, unless the path encodes the name of a specific series, in which case this refers to the file without the series included
+	 * File path if possible, or a URI otherwise.
 	 */
-	private String filePath;
-		
+	private String filePathOrUrl;
+
 	/**
 	 * Fix issue related to VSI images having (wrong) z-slices
 	 */
@@ -314,20 +314,20 @@ static BioFormatsImageServer checkSupport(URI uri, final BioFormatsServerOptions
 		// Try to get a local file path, but accept something else (since Bio-Formats handles other URIs)
 		try {
 			var path = GeneralTools.toPath(uri);
-			if (path != null)
-				filePath = path.toString();
-//			filePath = Paths.get(uri).toString();
+			if (path != null) {
+				filePathOrUrl = path.toString();
+			}
 		} catch (Exception e) {
 			logger.error(e.getLocalizedMessage(), e);
 		} finally {
-			if (filePath == null) {
+			if (filePathOrUrl == null) {
 				logger.debug("Using URI as file path: {}", uri);
-				filePath = uri.toString();
+				filePathOrUrl = uri.toString();
 			}
 		}
 
 		// Create a reader & extract the metadata
-		readerPool = new ReaderPool(options, filePath, bfArgs);
+		readerPool = new ReaderPool(options, filePathOrUrl, bfArgs);
 		IFormatReader reader = readerPool.getMainReader();
 		var meta = (OMEPyramidStore)reader.getMetadataStore();
 
@@ -986,7 +986,7 @@ public BufferedImage getAssociatedImage(String name) {
 	 * @return
 	 */
 	public File getFile() {
-		return filePath == null ? null : new File(filePath);
+		return filePathOrUrl == null ? null : new File(filePathOrUrl);
 	}
 
 
@@ -1160,8 +1160,10 @@ private IFormatReader createReader(final BioFormatsServerOptions options, final
 			Memoizer memoizer = null;
 			int memoizationTimeMillis = options.getMemoizationTimeMillis();
 			File dir = null;
-			// We can only use memoization if we don't have an illegal character
-			if (BioFormatsServerOptions.allowMemoization() && memoizationTimeMillis >= 0 && !id.contains(":")) {
+			File fileMemo = null;
+			boolean useTempMemoDirectory = false;
+			// Check if we want to (and can) use memoization
+			if (BioFormatsServerOptions.allowMemoization() && memoizationTimeMillis >= 0) {
 				// Try to use a specified directory
 				String pathMemoization = options.getPathMemoization();
 				if (pathMemoization != null && !pathMemoization.trim().isEmpty()) {
@@ -1173,10 +1175,22 @@ private IFormatReader createReader(final BioFormatsServerOptions options, final
 				}
 				if (dir == null) {
 					dir = getTempMemoDir(true);
+					useTempMemoDirectory = dir != null;
 				}
 				if (dir != null) {
-					memoizer = new Memoizer(imageReader, memoizationTimeMillis, dir);
-					imageReader = memoizer;
+					try {
+						memoizer = new Memoizer(imageReader, memoizationTimeMillis, dir);
+						fileMemo = memoizer.getMemoFile(id);
+						// The call to .toPath() should throw an InvalidPathException if there are illegal characters
+						// If so, we want to know that now before committing to the memoizer
+						if (fileMemo != null && fileMemo.toPath() != null)
+							imageReader = memoizer;
+					} catch (Exception e) {
+						logger.warn("Unable to use memoization: {}", e.getLocalizedMessage());
+						logger.debug(e.getLocalizedMessage(), e);
+						fileMemo = null;
+						memoizer = null;
+					}
 				}
 			}
 
@@ -1194,10 +1208,9 @@ private IFormatReader createReader(final BioFormatsServerOptions options, final
 
 
 			if (id != null) {
-				if (memoizer != null) {
-					File fileMemo = ((Memoizer)imageReader).getMemoFile(id);
-					// If we're using a temporary directory, delete the memo file
-					if (dir == getTempMemoDir(false))
+				if (fileMemo != null) {
+					// If we're using a temporary directory, delete the memo file when app closes
+					if (useTempMemoDirectory)
 						tempMemoFiles.add(fileMemo);
 
 					long memoizationFileSize = fileMemo == null ? 0L : fileMemo.length();
@@ -1248,6 +1261,7 @@ else if (!memoFileExists)
 
 			return imageReader;
 		}
+
 
 
 		private IFormatReader nextQueuedReader() throws InterruptedException {

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

@@ -120,7 +120,7 @@ public void installExtension(QuPathGUI qupath) {
 		// Add preferences to QuPath GUI
 		PreferencePane prefs = QuPathGUI.getInstance().getPreferencePane();
 		prefs.addPropertyPreference(enableBioformats, Boolean.class, "Enable Bio-Formats", "Bio-Formats", "Allow QuPath to use Bio-Formats for image reading");
-		prefs.addPropertyPreference(filesOnly, Boolean.class, "Local files only", "Bio-Formats", "Limit Bio-Formats to only opening local files, not other URLs.\n"
+		prefs.addPropertyPreference(filesOnly, Boolean.class, "Bio-Formats files only", "Bio-Formats", "Limit Bio-Formats to only opening files, not other URLs.\n"
 				+ "Allowing Bio-Formats to open URLs can cause performance issues if this results in attempting to open URLs intended to be read using other image servers.");
 		prefs.addPropertyPreference(useParallelization, Boolean.class, "Enable Bio-Formats tile parallelization", "Bio-Formats", "Enable reading image tiles in parallel when using Bio-Formats");
 //		prefs.addPropertyPreference(parallelizeMultichannel, Boolean.class, "Enable Bio-Formats channel parallelization (experimental)", "Bio-Formats", "Request multiple image channels in parallel, even if parallelization of tiles is turned off - "

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

@@ -105,6 +105,7 @@ private static float supportLevel(URI uri, String... args) {
 		BioFormatsServerOptions options = BioFormatsServerOptions.getInstance();
 
 		if (type.isURL() && options.getFilesOnly()) {
+			logger.debug("Cannot open URL with Bio-Formats - 'Bio-Formats files only' preference is turned on");
 			return 0;
 		}
 

qupath-gui-fx/src/main/java/qupath/lib/gui/panes/PreferencePane.java

@@ -803,7 +803,7 @@ static class DirectoryPropertyItem extends PropertyItem {
 
 		DirectoryPropertyItem(final Property<String> prop) {
 			this.prop = prop;
-			fileValue = Bindings.createObjectBinding(() -> prop.getValue() == null ? null : new File(prop.getValue()), prop);
+			fileValue = Bindings.createObjectBinding(() -> prop.getValue() == null || prop.getValue().isEmpty() ? null : new File(prop.getValue()), prop);
 		}
 
 		@Override
@@ -818,9 +818,9 @@ public Object getValue() {
 
 		@Override
 		public void setValue(Object value) {
-			if (value instanceof String)
+			if (value instanceof String) {
 				prop.setValue((String)value);
-			else if (value instanceof File)
+			} else if (value instanceof File)
 				prop.setValue(((File)value).getAbsolutePath());
 			else if (value == null)
 				prop.setValue(null);