Merge pull request #90 from BioImageTools/dataset-lifecycle-tobi

Add Open Resolution Level command and Pyramidal dataset lifecycle management

Author: stefanhahmann

src/main/java/sc/fiji/ome/zarr/open/ZarrOpenActions.java

@@ -46,18 +46,20 @@
 import java.util.Collections;
 import java.util.function.Consumer;
 import java.util.function.Function;
+import java.util.function.Supplier;
 
 import com.google.gson.JsonSyntaxException;
 
 import net.imglib2.img.Img;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.util.Cast;
 
-import bdv.util.BdvFunctions;
 import ij.IJ;
 import sc.fiji.ome.zarr.pyramid.Pyramidal5DImageDataImpl;
+import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
 import sc.fiji.ome.zarr.pyramid.exceptions.MultiImageDatasetException;
 import sc.fiji.ome.zarr.pyramid.exceptions.NoMatchingResolutionException;
+import sc.fiji.ome.zarr.pyramid.exceptions.NonExistingResolutionLevelException;
 import sc.fiji.ome.zarr.pyramid.exceptions.NotAMultiscaleImageException;
 import sc.fiji.ome.zarr.pyramid.exceptions.NotASingleScaleImageException;
 import sc.fiji.ome.zarr.pyramid.PyramidalDataset;
@@ -66,6 +68,7 @@
 import sc.fiji.ome.zarr.open.options.ZarrOpenBehavior;
 import sc.fiji.ome.zarr.open.options.ZarrReaderBackend;
 import sc.fiji.ome.zarr.ui.DnDActionChooser;
+import sc.fiji.ome.zarr.util.PyramidalService;
 import sc.fiji.ome.zarr.util.BdvUtils;
 import sc.fiji.ome.zarr.util.ScriptUtils;
 
@@ -83,6 +86,8 @@ public class ZarrOpenActions
 
 	private final ZarrOpeningSettings settings;
 
+	private Pyramidal5DImageDataImpl< ?, ? > cachedPyramid;
+
 	/**
 	 * Loads {@link ZarrOpeningSettings} from {@code context} and opens
 	 * {@code inputUri} via the action selected by the user's configured
@@ -166,23 +171,131 @@ public void openViewerDialog()
 
 	public Object openIJWithImage()
 	{
-		return openImage(
-				pyramidalDataset -> {
-					context.getService( UIService.class ).show( pyramidalDataset );
-					return null;
-				},
-				singleScaleImage -> ImageJFunctions.show( Cast.unchecked( singleScaleImage ) ),
-				"ImageJ"
-		);
+		try
+		{
+			return openPyramidImage(
+					() -> {
+						final PyramidalDataset dataset = getPyramid().asPyramidalDataset();
+						context.getService( UIService.class ).show( dataset );
+						logger.info( "Opened dataset in ImageJ: {}", inputUri );
+						return null;
+					},
+					singleScaleImage -> ImageJFunctions.show( Cast.unchecked( singleScaleImage ) ) );
+		}
+		catch ( NoMatchingResolutionException e )
+		{
+			showNonMatchingResolutionError( e );
+		}
+		return null;
+	}
+
+	/**
+	 * Opens the resolution level at {@code resolutionLevel} index as a new ImageJ dataset.
+	 * Index 0 is the highest resolution; each increment is the next coarser level.
+	 * <p>
+	 * Multiple calls — whether at the same or different level indices — each produce a separate
+	 * ImageJ {@code Dataset} (and a separate window), but all of them are backed by the same
+	 * {@link sc.fiji.ome.zarr.pyramid.Pyramidal5DImageData} object. The underlying
+	 * cached cell images and volatile images in
+	 * {@link sc.fiji.ome.zarr.pyramid.backend.PyramidContents} are the single source of truth
+	 * and are never loaded more than once per resolution level.
+	 *
+	 * @param resolutionLevel 0-based index into the resolution pyramid
+	 */
+	public Object openIJWithImage( final int resolutionLevel )
+	{
+		try
+		{
+			return openPyramidImage(
+					() -> {
+						final PyramidalDataset dataset = getPyramid().asPyramidalDataset( resolutionLevel );
+						context.getService( UIService.class ).show( dataset );
+						logger.info( "Opened dataset at resolution level {} in ImageJ: {}", resolutionLevel, inputUri );
+						return null;
+					},
+					singleScaleImage -> ImageJFunctions.show( Cast.unchecked( singleScaleImage ) ) );
+		}
+		catch ( NonExistingResolutionLevelException e )
+		{
+			showNonExistingResolutionLevelError( e );
+		}
+		return null;
 	}
 
 	public Object openBDVWithImage()
 	{
-		return openImage(
-				BdvUtils::showBdvAndRegisterDataset,
-				singleScaleImage -> BdvFunctions.show( singleScaleImage, "Image" ),
-				"BigDataViewer"
-		);
+		try
+		{
+			return openPyramidImage(
+					() -> {
+						final PyramidalBdv< ? > dataset = new PyramidalBdv<>( getPyramid() );
+						final PyramidalService pyramidalService = context.getService( PyramidalService.class );
+						final Object result = BdvUtils.showBdvAndRegisterDataset( dataset, pyramidalService );
+						logger.info( "Opened dataset in BigDataViewer: {}", inputUri );
+						return result;
+					},
+					singleScaleImage -> null );
+		}
+		catch ( NoMatchingResolutionException e )
+		{
+			showNonMatchingResolutionError( e );
+		}
+		return null;
+	}
+
+	private Pyramidal5DImageDataImpl< ?, ? > getPyramid()
+	{
+		if ( cachedPyramid == null )
+		{
+			final Integer preferredWidth;
+			if ( settings == null || settings.getOpenBehavior().equals( ZarrOpenBehavior.IMAGEJ_HIGHEST_RESOLUTION ) )
+				preferredWidth = null;
+			else
+				preferredWidth = settings.getPreferredMaxWidth();
+
+			final ZarrReaderBackend backend = settings == null
+					? ZarrOpeningSettings.DEFAULT_READER_BACKEND
+					: settings.getReaderBackend();
+			switch ( backend )
+			{
+			case ZARR_JAVA:
+			{
+				@SuppressWarnings( { "rawtypes", "unchecked" } )
+				final Pyramidal5DImageDataImpl< ?, ? > zarrJavaData =
+						new Pyramidal5DImageDataImpl( context, new ZarrJavaPyramidBackend( inputUri ) );
+				cachedPyramid = zarrJavaData;
+				break;
+			}
+			case N5:
+			default:
+				cachedPyramid = new Pyramidal5DImageDataImpl<>( context, inputUri, preferredWidth );
+				break;
+			}
+		}
+		return cachedPyramid;
+	}
+
+	private Object openPyramidImage( final Supplier< Object > multiScaleOpener, final Function< Img< ? >, Object > singleScaleOpener )
+	{
+		try
+		{
+			return multiScaleOpener.get();
+		}
+		catch ( MultiImageDatasetException e )
+		{
+			showMultiImageNotSupported( e );
+		}
+		catch ( NotAMultiscaleImageException e )
+		{
+			logger.warn( "Not a multiscale image: {}", e.getMessage() );
+			showSingleScaleNotSupported();
+			// TODO: openSingleScaleImage( singleScaleOpener ) when single-scale support is added
+		}
+		catch ( IllegalArgumentException | JsonSyntaxException e )
+		{
+			showNonZarrError( e );
+		}
+		return null;
 	}
 
 	private void showMultiImageNotSupported( final MultiImageDatasetException e )
@@ -220,83 +333,33 @@ private void showNonMatchingResolutionError( final Exception e )
 		logger.warn( "Not opening dataset: {}. Error message: {}", inputUri, e.getMessage() );
 	}
 
-	Object openImage( final Function< PyramidalDataset< ? >, Object > multiScaleImageOpener,
-			final Function< Img< ? >, Object > singleScaleImageOpener,
-			final String message )
+	private void showNonExistingResolutionLevelError( final NonExistingResolutionLevelException e )
+	{
+		errorHandler.accept( "Could not open resolution level from dataset: " + inputUri + "\n\n" + e.getMessage() );
+		logger.warn( "Could not open resolution level: {}. Error message: {}", inputUri, e.getMessage() );
+	}
+
+	Object openImage( final Function< PyramidalDataset, Object > multiScaleImageOpener,
+			final Function< Img< ? >, Object > singleScaleImageOpener )
 	{
 		try
 		{
-			Object result = openMultiScaleImage( multiScaleImageOpener );
-			logger.info( "Opened dataset in {}: {}", message, inputUri );
-			return result;
-		}
-		catch ( MultiImageDatasetException e )
-		{
-			logger.warn( "Tried to open a multi image dataset: {}", e.getMessage() );
-			showMultiImageNotSupported( e );
-		}
-		catch ( NotAMultiscaleImageException e )
-		{
-			logger.warn( "Not a multiscale image: {}", e.getMessage() );
-			logger.info( "Try opening as single-scale image instead." );
-			try
-			{
-				showSingleScaleNotSupported();
-				//Object result = openSingleScaleImage( singleScaleImageOpener ); // currently not supported
-				//logger.info( "Opened single scale image in {}: {}", message, inputUri );
-				return null;
-			}
-			catch ( NotASingleScaleImageException ex )
-			{
-				showSingleScaleError( ex );
-			}
+			return openPyramidImage(
+					() -> {
+						final PyramidalDataset dataset = getPyramid().asPyramidalDataset();
+						final Object result = multiScaleImageOpener.apply( dataset );
+						logger.info( "Opened dataset: {}", inputUri );
+						return result;
+					},
+					singleScaleImageOpener );
 		}
 		catch ( NoMatchingResolutionException e )
 		{
 			showNonMatchingResolutionError( e );
 		}
-		catch ( IllegalArgumentException | JsonSyntaxException e )
-		{
-			showNonZarrError( e );
-		}
 		return null;
 	}
 
-	private Object openMultiScaleImage( final Function< PyramidalDataset< ? >, Object > multiScaleImageOpener )
-			throws NotAMultiscaleImageException, NoMatchingResolutionException
-	{
-		final Integer preferredWidth;
-		if ( settings == null || settings.getOpenBehavior().equals( ZarrOpenBehavior.IMAGEJ_HIGHEST_RESOLUTION ) )
-			preferredWidth = null;
-		else
-			preferredWidth = settings.getPreferredMaxWidth();
-
-		final ZarrReaderBackend backend = settings == null
-				? ZarrOpeningSettings.DEFAULT_READER_BACKEND
-				: settings.getReaderBackend();
-
-		final Pyramidal5DImageDataImpl< ?, ? > data;
-		switch ( backend )
-		{
-		case ZARR_JAVA:
-		{
-			@SuppressWarnings( { "rawtypes", "unchecked" } )
-			final Pyramidal5DImageDataImpl< ?, ? > zarrJavaData =
-					new Pyramidal5DImageDataImpl( context, new ZarrJavaPyramidBackend( inputUri ) );
-			data = zarrJavaData;
-			break;
-		}
-		case N5:
-		default:
-			data = new Pyramidal5DImageDataImpl<>( context, inputUri, preferredWidth );
-			break;
-		}
-
-		final Object result = multiScaleImageOpener.apply( data.asPyramidalDataset() );
-		logger.info( "Opened multiscale image with {} backend: {}", backend, inputUri );
-		return result;
-	}
-
 	private Object openSingleScaleImage( final Function< Img< ? >, Object > singleScaleImageOpener ) throws NotASingleScaleImageException
 	{
 		N5Reader reader = new N5Factory().openReader( inputUri.toString() );

src/main/java/sc/fiji/ome/zarr/plugins/DnDHandlerPlugin.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -48,7 +48,6 @@
 import java.util.ArrayList;
 
 import sc.fiji.ome.zarr.open.ZarrOpenActions;
-import sc.fiji.ome.zarr.util.BdvHandleService;
 import sc.fiji.ome.zarr.util.ZarrUtils;
 
 @Plugin( type = IOPlugin.class, attrs = @Attr( name = "eager" ) )
@@ -59,9 +58,6 @@ public class DnDHandlerPlugin extends AbstractIOPlugin< Object >
 	//the "innocent" product of the (hypothetical) file reading... which Fiji will not display
 	private static final Object FAKE_INPUT = new ArrayList<>( 0 );
 
-	@Parameter
-	private BdvHandleService bdvHandleService; //TODO, is it really used down-stream?
-
 	@Parameter
 	private PrefService prefService;
 

src/main/java/sc/fiji/ome/zarr/plugins/OpenInBDVCommand.java

@@ -6,13 +6,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- * 
+ *
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- * 
+ *
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -28,42 +28,45 @@
  */
 package sc.fiji.ome.zarr.plugins;
 
-import net.imagej.Dataset;
-import net.imglib2.util.Cast;
+import java.lang.invoke.MethodHandles;
 
 import org.scijava.command.Command;
-import org.scijava.log.LogLevel;
-import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
+import org.scijava.ui.UIService;
 
-import sc.fiji.ome.zarr.pyramid.PyramidalDataset;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import sc.fiji.ome.zarr.pyramid.Pyramidal;
+import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
+import sc.fiji.ome.zarr.util.PyramidalService;
 import sc.fiji.ome.zarr.util.BdvUtils;
 
 @Plugin( type = Command.class, menuPath = "Plugins > OME-Zarr > Open Current OME-Zarr Image in BigDataViewer" )
 public class OpenInBDVCommand implements Command
 {
-	@Parameter
-	LogService logService;
+	private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
 	@Parameter
-	public Dataset dataset;
+	private UIService uiService;
+
+	@Parameter( required = false )
+	private PyramidalService pyramidalService;
+
+	@Parameter( required = false )
+	private Pyramidal pyramidal;
 
 	@Override
 	public void run()
 	{
-		logService.log( LogLevel.DEBUG, "Trying to open: " + dataset.getName() );
-		logService.log( LogLevel.DEBUG, "Class: " + dataset.getClass() );
-		logService.log( LogLevel.DEBUG, "Dataset instanceof PyramidalDataset: " + ( dataset instanceof PyramidalDataset ) );
-		if ( dataset instanceof PyramidalDataset )
-		{
-			logService.log( 0, "Opening " + dataset.getClass() + " in BDV..." );
-			PyramidalDataset< ? > pyramidalDataset = Cast.unchecked( dataset );
-			BdvUtils.showBdvAndRegisterDataset( pyramidalDataset );
-		}
-		else
+		logger.trace( "Running OpenInBDVCommand. pyramidal={}", pyramidal );
+		if ( pyramidal == null )
 		{
-			logService.error( "Cannot display datasets of type " + dataset.getClass() + " in BDV." );
+			uiService.showDialog( "The active image is not an OME-Zarr dataset.", "Open in BigDataViewer" );
+			return;
 		}
+		final PyramidalBdv< ? > bdvDataset = new PyramidalBdv<>( pyramidal.getPyramidal5DImageData() );
+		BdvUtils.showBdvAndRegisterDataset( bdvDataset, pyramidalService );
 	}
 }