Fix: Image parsers parsing RAI/ImgPlus but initializing on ImagePlus...

... This makes this commands available in stream mode

Author: tferr

src/main/java/sc/fiji/snt/DelineationsManager.java

@@ -647,17 +647,17 @@ JPopupMenu importMenu() {
             if (sntui.noPathsError()) return;
             final ImagePlus labelImp = getLabelImage();
             if (labelImp == null) return;
-            final ImagePlus tracingImp = sntui.plugin.getImagePlus();
-            if (tracingImp != null) {
-                final boolean dimMatch = labelImp.getWidth() == tracingImp.getWidth()
-                        && labelImp.getHeight() == tracingImp.getHeight()
-                        && labelImp.getNSlices() == tracingImp.getNSlices();
+            // NB: not plugin.getImagePlus() != null -- that is null in Stream mode!
+            if (sntui.plugin.accessToValidImageData()) {
+                final int[] fullDims = sntui.plugin.getFullImageDimensions();
+                final boolean dimMatch = labelImp.getWidth() == fullDims[0]
+                        && labelImp.getHeight() == fullDims[1]
+                        && labelImp.getNSlices() == fullDims[2];
                 if (!dimMatch && !sntui.guiUtils.getConfirmation(
                         "The label image dimensions (" + labelImp.getWidth() + "×"
                                 + labelImp.getHeight() + "×" + labelImp.getNSlices()
                                 + ") do not match the tracing image ("
-                                + tracingImp.getWidth() + "×" + tracingImp.getHeight()
-                                + "×" + tracingImp.getNSlices()
+                                + fullDims[0] + "×" + fullDims[1] + "×" + fullDims[2]
                                 + "). Assignments may be incorrect. Proceed anyway?",
                         "Dimension Mismatch")) {
                     return;

src/main/java/sc/fiji/snt/SNT.java

@@ -4415,22 +4415,28 @@ public void loadSecondaryImage(final File file) throws IOException, IllegalArgum
 		// Falls back to the conventional path for anything it can't resolve
 		// (resolvePathToSource() itself ends in a conventional ImgPlus-open fallback too, but keeping
 		// our own fallback here avoids any behavior change for formats that already worked before).
-		RandomAccessibleInterval<?> data = null;
+		// Resolution and dimension-checking are deliberately two separate steps here: only a failure to
+		// resolve/parse the source at all should fall back to the conventional (RAM-unsafe-for-big-data)
+		// path below. A dimension mismatch on an already-resolved big-data source must NOT fall back to it
+		Object resolvedSource = null;
 		try {
-			data = extractSecondaryData(SpimDataUtils.resolvePathToSource(file.getAbsolutePath()));
+			resolvedSource = SpimDataUtils.resolvePathToSource(file.getAbsolutePath());
 		} catch (final Exception e) {
 			SNTUtils.log("Secondary layer: '" + file.getName() + "' could not be resolved as a big-data "
 					+ "container (" + e.getMessage() + "); falling back to conventional image opening");
 		}
-		if (data != null) {
-			// computeStatistics=false: data here may be a lazily-backed (N5/Zarr/BDV) source, and eager
-			// min/max/mean/stdDev via generic OpService calls is 3 separate full-volume passes -- real
-			// disk I/O per chunk, done 3x over, with no caching between passes. That may work for the
-			// classic ImagePlus but not for lazy data.
-			//noinspection unchecked,rawtypes
-			loadSecondaryImage((RandomAccessibleInterval) data, true, false);
-			setSecondaryImage(isSecondaryDataAvailable() ? file : null);
-			return;
+		if (resolvedSource != null) {
+			final RandomAccessibleInterval<?> data = extractSecondaryData(resolvedSource);
+			if (data != null) {
+				// computeStatistics=false: data here may be a lazily-backed (N5/Zarr/BDV) source, and eager
+				// min/max/mean/stdDev via generic OpService calls is 3 separate full-volume passes -- real
+				// disk I/O per chunk, done 3x over, with no caching between passes. That may work for the
+				// classic ImagePlus but not for lazy data.
+				//noinspection unchecked,rawtypes
+				loadSecondaryImage((RandomAccessibleInterval) data, true, false);
+				setSecondaryImage(isSecondaryDataAvailable() ? file : null);
+				return;
+			}
 		}
 		final ImagePlus imp = openCachedDataImage(file);
 		loadSecondaryImage(imp, true);
@@ -4440,14 +4446,24 @@ public void loadSecondaryImage(final File file) throws IOException, IllegalArgum
 	/**
 	 * Extracts a {@link RandomAccessibleInterval} for the currently active channel/frame from a
 	 * resolved big-data source (see {@link SpimDataUtils#resolvePathToSource(String)}), or
-	 * {@code null} if {@code source} isn't one of the recognized types, or its XYZ dimensions don't
-	 * match the data currently being traced (see {@link #sameXYZDimensionsAsTracingData}).
+	 * {@code null} if {@code source} isn't one of the recognized types (the caller, {@link
+	 * #loadSecondaryImage(File)}, then falls back to conventional image opening).
+	 * <p>
+	 * If {@code source} <i>is</i> one of the recognized types but its XYZ dimensions don't match the
+	 * data currently being traced (see {@link #sameXYZDimensionsAsTracingData}), this throws instead
+	 * of returning {@code null}: unlike a genuinely unresolved source, this data was already
+	 * successfully resolved as big data, so silently falling back to the conventional path would mean
+	 * fully loading a potentially huge dataset into RAM via SCIFIO/Bio-Formats just to discover its
+	 * dimensions are wrong. Failing fast here, with the same message {@link #openCachedDataImage(File)}
+	 * gives for the same condition, avoids that.
 	 * <p>
 	 * For {@link AbstractSpimData} (BDV .xml/IMS) and {@link SpimDataUtils.N5Sources} (ambiguous
 	 * N5/Zarr layouts), only the first setup/source and timepoint 0 are used. This is the same
 	 * simplification {@code BigDataLoaderCmd#applyFallbackCalibration} already makes for the
 	 * <i>primary</i> volume in this same situation. A genuinely multichannel secondary layer of
 	 * either of these types would thus only expose its first channel.
+	 *
+	 * @throws IllegalArgumentException if the resolved source's dimensions don't match the data currently being traced
 	 */
 	private RandomAccessibleInterval<?> extractSecondaryData(final Object source) {
 		final RandomAccessibleInterval<?> data;
@@ -4473,9 +4489,10 @@ private RandomAccessibleInterval<?> extractSecondaryData(final Object source) {
                 return null; // unresolved / unrecognized type
             }
         }
-		if (!sameXYZDimensionsAsTracingData(data)) {
-			SNTUtils.log("Secondary layer: dimensions do not match those of the data being traced");
-			return null;
+		if (!sameXYZDimensionsAsTracingData(data)) { // NB: throws rather than returning null
+			final String msg = (isStreamMode())
+					? "" : " If this is unexpected, check under 'Image>Properties...' that CZT axes are not swapped.";
+			throw new IllegalArgumentException("Dimensions do not match those of the image being traced." + msg);
 		}
 		return data;
 	}
@@ -4673,9 +4690,9 @@ private ImagePlus openCachedDataImage(final File file) throws IOException {
 		if (!sameXYZDimensionsAsTracingData(imp)) {
 			// We are imposing only XYZ dimensions to e.g., allow for loading of single-channel
 			// p-maps. Hopefully, being lax about CT dimensions won't cause issues downstream
-			final String refName = (xy != null) ? xy.getTitle() : "the image being traced";
-			throw new IllegalArgumentException("Dimensions do not match those of " + refName
-					+ ". If this is unexpected, check under 'Image>Properties...' that CZT axes are not swapped.");
+			final String msg = (isStreamMode())
+					? "" : " If this is unexpected, check under 'Image>Properties...' that CZT axes are not swapped.";
+			throw new IllegalArgumentException("Dimensions do not match those of the image being traced." + msg);
 		}
 		return imp;
 	}

src/main/java/sc/fiji/snt/SNTUI.java

@@ -3257,7 +3257,6 @@ private JPanel secondaryDataPanel() {
         commandFinder.register(mi2, "Main tab", "Interactive tracing (II Layer)");
         final JMenuItem mi3 = GuiUtils.MenuItems.fromFileImage();
         mi3.addActionListener(e -> loadSecondaryImage(false));
-        mi2.setEnabled(!plugin.isStreamMode()); // ChooseDatasetCmd is not yet ready for OME-ZARR/N5 etc. disable for now
         commandFinder.register(mi3, "Main tab", "Interactive tracing (II Layer)");
         final JMenuItem mi4 = new JMenuItem("Flush Current Layer...", IconFactory.menuIcon(IconFactory.GLYPH.TOILET));
         registerInCommandFinder(mi4, "Flush Secondary Layer", "Main tab", "Interactive tracing");
@@ -3346,7 +3345,12 @@ private void loadSecondaryImage(final boolean fromAlreadyOpenImageOtherwiseFile)
             warnOnAutoCTcompatibilityOthers();
             final File proposedFile = (plugin.getFilteredImageFile() == null) ? plugin.getPrefs().getRecentDir()
                     : plugin.getFilteredImageFile();
-            final File file = guiUtils.getOpenFile("Choose Secondary Image", proposedFile);
+            // An N5/OME-Zarr secondary layer is a directory, not a single file, and SNT#loadSecondaryImage(File)
+            // (via SpimDataUtils#resolvePathToSource) supports resolving one
+            final File file = (plugin.isStreamMode())
+                    ? guiUtils.getOpenFileOrDirectory("Choose Secondary Image", proposedFile)
+                    : guiUtils.getOpenFile("Choose Secondary Image", proposedFile);
+
             if (file != null)
                 loadSecondaryImageFile(file);
         }

src/main/java/sc/fiji/snt/gui/GuiUtils.java

@@ -1271,6 +1271,22 @@ public File getOpenFile(final String title, final File file, final String... all
 		return (File) showOpenDialog(title, JFileChooser.FILES_ONLY, false, file, false, filter);
 	}
 
+	/**
+	 * As {@link #getOpenFile(String, File, String...)}, but the dialog also allows selecting a
+	 * directory directly. Needed for pointing directly at an N5/OME-Zarr container; a metadata file
+	 * *inside* such a container (e.g. {@code zarr.json}, {@code .zattrs}) can still be selected too.
+	 * Both resolve to the same container root,
+	 * <p>
+	 * NB: unlike most {@code getXxxFile(s)} methods above, this always uses the classic chooser and
+	 * ignores {@link SNTPrefs#getUseNativeFileChooser()} -- FlatLaf's {@link SystemFileChooser} (the
+	 * native alternative) does not support a mixed files-and-directories selection mode at all.
+	 */
+	public File getOpenFileOrDirectory(final String title, final File file) {
+		final JFileChooser chooser = fileChooser(title, file, JFileChooser.OPEN_DIALOG,
+				JFileChooser.FILES_AND_DIRECTORIES);
+		return (File) getOpenFileChooserResult(chooser);
+	}
+
 	public File getSaveFile(final String title, final File file, final String... allowedExtensions) {
 		File chosenFile = null;
 		final JFileChooser chooser = fileChooser(title, file, JFileChooser.SAVE_DIALOG, JFileChooser.FILES_ONLY);

src/main/java/sc/fiji/snt/gui/cmds/AlongPathDetectorCmd.java

@@ -24,6 +24,7 @@
 
 import ij.ImagePlus;
 import ij.plugin.frame.RoiManager;
+import net.imagej.Dataset;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.RealType;
 import org.scijava.command.Command;
@@ -110,16 +111,17 @@ private void init() {
 
         channel = snt.getChannel();
 
-        final boolean hasImage = snt.accessToValidImageData()
-                && snt.getImagePlus() != null;
+        // NB: not snt.getImagePlus() != null -- that is null in Stream mode unless a materialized crop is active
+        final Dataset dataset = snt.accessToValidImageData() ? snt.getDataset() : null;
+        final boolean hasImage = dataset != null;
 
         if (hasImage) {
-            if (snt.getImagePlus().getNChannels() == 1) {
+            if (dataset.getChannels() == 1) {
                 resolveInput("channel");
             } else {
                 final MutableModuleItem<Integer> mItem = getInfo()
                         .getMutableInput("channel", Integer.class);
-                mItem.setMaximumValue(snt.getImagePlus().getNChannels());
+                mItem.setMaximumValue((int) dataset.getChannels());
             }
         } else {
             // No image: force intensity filtering off and hide related params
@@ -161,7 +163,8 @@ public void run() {
         final RandomAccessibleInterval<? extends RealType<?>> intensityImg;
         double resolvedMinIntensity = minIntensity;
         if (useIntensity) {
-            if (snt == null || !snt.accessToValidImageData() || snt.getImagePlus() == null) {
+            // NB: not snt.getImagePlus() == null -- see the same note in init() above
+            if (snt == null || !snt.accessToValidImageData()) {
                 error("Intensity filtering requires valid image data to be loaded.");
                 return;
             }
@@ -175,8 +178,15 @@ public void run() {
             }
             if (snt.getChannel() == channel) {
                 intensityImg = snt.getLoadedData();
-            } else {
+            } else if (snt.getImagePlus() != null) {
                 intensityImg = ImgUtils.getCtSlice3d(snt.getImagePlus(), channel, snt.getFrame());
+            } else {
+                // Stream mode without a materialized crop: only the active channel's data is resident
+                // (see SNT#getDataset()), so a different channel genuinely cannot be sampled here
+                error("Intensity filtering on a channel other than the active one (" + snt.getChannel() + ")"
+                        + " requires either a materialized crop or Classic mode. Set 'Intensity channel' to "
+                        + snt.getChannel() + ", or filter using radius only (Min. intensity = 0).");
+                return;
             }
         } else {
             intensityImg = null;

src/main/java/sc/fiji/snt/gui/cmds/LabelProximityDetectorCmd.java

@@ -99,12 +99,15 @@ private void init() {
                 continue; // skip binary and hyperstacks; only first C/T would be used
 
             // Quick dimension check: label image should match tracing image spatially
-            final ImagePlus tracingImp = snt.getImagePlus();
-            if (tracingImp != null) {
-                if (imp.getWidth() != tracingImp.getWidth() || imp.getHeight() != tracingImp.getHeight()) {
+            // NB: not snt.getImagePlus() != null -- that is null in Stream mode unless a materialized
+            // crop is active, which would let every open image through unfiltered in that case.
+            // getFullImageDimensions() resolves correctly in every mode (Classic, Stream, materialized crop)
+            if (snt.accessToValidImageData()) {
+                final int[] fullDims = snt.getFullImageDimensions();
+                if (imp.getWidth() != fullDims[0] || imp.getHeight() != fullDims[1]) {
                     continue;
                 }
-                if (tracingImp.getNSlices() > 1 && imp.getNSlices() != tracingImp.getNSlices()) {
+                if (fullDims[2] > 1 && imp.getNSlices() != fullDims[2]) {
                     continue;
                 }
             }
@@ -151,10 +154,16 @@ public void run() {
         }
 
         // Dimension check against tracing data
-        final ImagePlus tracingImp = snt.getImagePlus();
-        if (tracingImp != null && !ImgUtils.haveSameSpatialDimensions(tracingImp, labelImg)) {
-            msg("Label image dimensions do not match the tracing image.\n"
-                    + "Results may be inaccurate.", "Dimension Mismatch");
+        // NB: not snt.getImagePlus() != null -- see the same note in init() above
+        if (snt.accessToValidImageData()) {
+            final int[] fullDims = snt.getFullImageDimensions();
+            final boolean dimMatch = labelImg.dimension(0) == fullDims[0]
+                    && labelImg.dimension(1) == fullDims[1]
+                    && (labelImg.numDimensions() <= 2 || labelImg.dimension(2) == fullDims[2]);
+            if (!dimMatch) {
+                msg("Label image dimensions do not match the tracing image.\n"
+                        + "Results may be inaccurate.", "Dimension Mismatch");
+            }
         }
 
         // Build config

src/main/java/sc/fiji/snt/gui/cmds/PeripathDetectorCmd.java

@@ -24,6 +24,7 @@
 
 import ij.ImagePlus;
 import ij.plugin.frame.RoiManager;
+import net.imagej.Dataset;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.RealType;
 import org.scijava.command.Command;
@@ -124,14 +125,18 @@ private void init() {
                         ? p.getFitted() : p)
                 .collect(Collectors.toList());
         channel = snt.getChannel();
-        if (snt.accessToValidImageData()) {
-            if (snt.getImagePlus() != null && snt.getImagePlus().getNChannels() == 1) {
+        // NB: not snt.getImagePlus() != null -- that is null in Stream mode unless a materialized crop
+        // is active. snt.getDataset() already handles that case: it falls back to a Dataset built from
+        // the currently-streamed data when no resident ImagePlus exists
+        final Dataset dataset = snt.accessToValidImageData() ? snt.getDataset() : null;
+        if (dataset != null) {
+            if (dataset.getChannels() == 1) {
                 // Only 1 channel available
                 resolveInput("channel");
             } else {
                 // Set channel max from loaded image
                 final MutableModuleItem<Integer> mItem = getInfo().getMutableInput("channel", Integer.class);
-                mItem.setMaximumValue((snt.getImagePlus() != null) ? snt.getImagePlus().getNChannels() : 1);
+                mItem.setMaximumValue((int) dataset.getChannels());
             }
             // Pre-fill prominence from image stats if available
             final double[] stats = new double[]{snt.getStats().min, snt.getStats().max};
@@ -173,7 +178,10 @@ public void run() {
             error("No paths selected for analysis.");
             return;
         }
-        if (snt == null || !snt.accessToValidImageData() || snt.getImagePlus() == null) {
+        // NB: not snt.getImagePlus() == null -- see the same note in init() above. Requiring only
+        // accessToValidImageData() lets detection work in Stream mode for the case of the currently active channel,
+        // via snt.getLoadedData() below
+        if (snt == null || !snt.accessToValidImageData()) {
             error("Maxima detection requires valid image data to be loaded.");
             return;
         }
@@ -182,8 +190,15 @@ public void run() {
         final RandomAccessibleInterval<? extends RealType<?>> detectionImg;
         if (snt.getChannel() == channel) {
             detectionImg = snt.getLoadedData();
-        } else {
+        } else if (snt.getImagePlus() != null) {
             detectionImg = ImgUtils.getCtSlice3d(snt.getImagePlus(), channel, snt.getFrame());
+        } else {
+            // Stream mode without a materialized crop: only the active channel's data is resident
+            // (see SNT#getDataset() javadoc), so a different channel genuinely cannot be sampled here
+            error("Detection on a channel other than the active one (" + snt.getChannel() + ")"
+                    + " requires either a materialized crop or Classic mode. Set 'Detection channel' to "
+                    + snt.getChannel() + ".");
+            return;
         }
 
         // Build config
@@ -252,6 +267,13 @@ public void run() {
         } else {
             // Add to ROI Manager: one grouped PointRoi per path
             final ImagePlus imp = snt.getImagePlus();
+            if (imp == null) {
+                // Stream mode without a materialized crop: no classic canvas for RoiManager/PointRoi to
+                // attach to (unlike detection itself above, this really has no Stream-mode equivalent)
+                error("ROI output requires an image canvas to be available (Classic mode, or a "
+                        + "materialized crop in Stream mode). Use 'Bookmarked locations' output instead.");
+                return;
+            }
             RoiManager rm = RoiManager.getInstance2();
             if (rm == null) rm = new RoiManager();
             for (final Map.Entry<Path, List<Detection>> entry : resultsByPath.entrySet()) {