Merge pull request #191 from saalfeldlab/perf/sharedN5

Perf/shared n5

Author: bogovicj

pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>41.0.0</version>
+		<version>44.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -118,6 +118,9 @@
 		<license.projectName>BigWarp plugin for Fiji.</license.projectName>
 		<license.excludes>**/resources/*.xml</license.excludes>
 
+		<scijava.jvm.version>8</scijava.jvm.version>
+		<scijava.jvm.build.version>[1.8.0-101,)</scijava.jvm.build.version>
+
 		<jcommander.version>1.48</jcommander.version>
 		<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
 

src/main/java/bdv/gui/BigWarpInitDialog.java

@@ -84,7 +84,6 @@
 import bigwarp.transforms.metadata.N5TransformMetadataParser;
 import bigwarp.transforms.metadata.N5TransformTreeCellRenderer;
 import ij.IJ;
-import ij.ImageJ;
 import ij.ImagePlus;
 import ij.Macro;
 import ij.Prefs;
@@ -157,7 +156,7 @@ public BigWarpInitDialog( final String title, final DatasetService datasetServic
 		initialPath = "";
 		imageJOpen = IJ.getInstance() != null;
 
-		buildN5SelectionDialog();
+		exec = Executors.newFixedThreadPool( Prefs.getThreads() );
         final Container content = getContentPane();
         content.add( createContent() );
         pack();
@@ -325,11 +324,12 @@ else if( tableRow.type.equals( SourceType.DATASET ))
 					BigWarpInit.add( data, infos, tableRow.getTransform(), tableRow.getTransformUri() );
 					id += infos.size();
 				}
-				else
+				else // URI
 				{
 					// deal with exceptions differently?
 					try
 					{
+						final N5Metadata metadata = sourceTableModel.getMetadata(i);
 						final LinkedHashMap< Source< T >, SourceInfo > infos = BigWarpInit.createSources( data, tableRow.srcName, id, tableRow.moving );
 						BigWarpInit.add( data, infos, tableRow.getTransform(), tableRow.getTransformUri() );
 						id += infos.size();
@@ -466,7 +466,6 @@ public JPanel createContent()
 		containerPathText = new JTextField();
 		containerPathText.setText( initialPath );
 		containerPathText.setPreferredSize( new Dimension( frameSizeX / 3, containerPathText.getPreferredSize().height ) );
-//		containerPathText.addActionListener( e -> openContainer( n5Fun, () -> getN5RootPath(), pathFun ) );
 		panel.add(containerPathText, gbcBar);
 
 		cadd.gridy = 2;
@@ -497,7 +496,7 @@ public JPanel createContent()
 
 		addN5Button.addActionListener( e -> {
 
-			selectionDialog = new DatasetSelectorDialog( new N5ViewerReaderFun(), new N5BasePathFun(),
+			selectionDialog = new DatasetSelectorDialog( new BigWarpInit.BigWarpN5ReaderFun(), new N5BasePathFun(),
 					lastOpenedContainer,
 					BigWarpInit.GROUP_PARSERS,
 					BigWarpInit.PARSERS);
@@ -660,59 +659,22 @@ public JPanel createContent()
 		return panel;
 	}
 
+	/**
+	 * This method is a no-op.
+	 *
+	 * @deprecated
+	 */
+	@Deprecated
 	public void buildN5SelectionDialog()
 	{
-		exec = Executors.newFixedThreadPool( Prefs.getThreads() );
-
-
-		/*
-		 * The Dialogs need to be created anew by the action listener
-		 */
-
-//		selectionDialog = new DatasetSelectorDialog( new N5ViewerReaderFun(), new N5BasePathFun(),
-//				lastOpenedContainer,
-//				n5vGroupParsers,
-//				n5Parsers);
-//
-//		selectionDialog.setLoaderExecutor( exec );
-//		selectionDialog.setTreeRenderer(new N5ViewerTreeCellRenderer(false));
-//
-//		selectionDialog.setContainerPathUpdateCallback( x -> {
-//			if ( x != null )
-//				lastOpenedContainer = x;
-//		} );
-//
-//		// figure this out
-////		selectionDialog.setCancelCallback( x -> {
-////			// set back recorder state if canceled
-////			Recorder.record = initialRecorderState;
-////		} );
-//
-//		selectionDialog.setVirtualOption( false );
-//		selectionDialog.setCropOption( false );
-
-
-//		// transform
-//
-//		final N5MetadataParser<?>[] tformParsers = new N5MetadataParser<?>[]{ new N5TransformMetadataParser() };
-//
-//		transformSelectionDialog = new DatasetSelectorDialog( new N5ViewerReaderFun(), new N5BasePathFun(),
-//				lastOpenedContainer, new N5MetadataParser[] {}, tformParsers );
-//
-//		transformSelectionDialog.setLoaderExecutor( exec );
-//		transformSelectionDialog.setTreeRenderer( new N5TransformTreeCellRenderer( true ) );
-//		transformSelectionDialog.setContainerPathUpdateCallback( x -> {
-//			if ( x != null )
-//				lastOpenedContainer = x;
-//		} );
-
+		// NoOp 
 	}
 
 	public void n5DialogCallback( final DataSelection selection )
 	{
 		final String n5RootPath = selectionDialog.getN5RootPath();
-		for( final N5Metadata m : selection.metadata )
-			sourceTableModel.add( n5RootPath + "?" + m.getPath() );
+		for (final N5Metadata m : selection.metadata)
+			sourceTableModel.add(n5RootPath + "?" + m.getPath(), m);
 
 		repaint();
 	}
@@ -948,7 +910,7 @@ private String browseTransformDialog()
 		return s;
 	}
 
-	public void setParameters( final String projectLandmarkPath, final String images, final String moving, final String transforms ) {
+	public void setParameters( final String projectLaBigWarpInitDialogndmarkPath, final String images, final String moving, final String transforms ) {
 		this.projectLandmarkPath = projectLandmarkPath;
 		this.imageList = images;
 		this.movingList = moving;

src/main/java/bdv/gui/sourceList/BigWarpSourceTableModel.java

@@ -27,7 +27,6 @@
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.util.ArrayList;
-import java.util.function.Consumer;
 import java.util.function.Function;
 import java.util.function.Supplier;
 
@@ -42,6 +41,7 @@
 import org.janelia.saalfeldlab.n5.N5URI;
 import org.janelia.saalfeldlab.n5.imglib2.N5DisplacementField;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
+import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
 
 import bigwarp.transforms.NgffTransformations;
 import net.imglib2.realtransform.RealTransform;
@@ -58,6 +58,9 @@ public static enum SourceType { IMAGEPLUS, DATASET, URL };
 	protected final ArrayList<SourceRow> sources;
 	protected final ArrayList<RemoveRowButton> rmRowButtons;
 
+	// not displayed
+	protected final ArrayList<N5Metadata> metadataList;
+
 	protected static int imageColIdx = 0;
 	protected static int movingColIdx = 1;
 	protected static int transformColIdx = 2;
@@ -78,6 +81,7 @@ public BigWarpSourceTableModel(final Function<String, String> transformChangedCa
 		columnNames = colNames;
 		sources = new ArrayList<>();
 		rmRowButtons = new ArrayList<>();
+		metadataList = new ArrayList<>();
 		this.transformChangedCallback = transformChangedCallback;
 	}
 
@@ -152,6 +156,11 @@ else if (col == transformColIdx)
 			setTransform(row, (String)value);
 	}
 
+	public N5Metadata getMetadata(int row) {
+
+		return metadataList.get(row);
+	}
+
 	public void setTransform(final int row, final String value) {
 
 		if (transformChangedCallback != null) {
@@ -164,11 +173,17 @@ public void setTransform(final int row, final String value) {
 			sources.get(row).transformUrl = value;
 	}
 
-	public void add(String srcName, boolean moving, SourceType type) {
-
+	public void add(String srcName, boolean moving, SourceType type, N5Metadata metadata)
+	{
 		final RemoveRowButton rmButton = new RemoveRowButton(sources.size());
 		rmRowButtons.add(rmButton);
 		sources.add(new SourceRow(srcName, moving, "", type));
+		metadataList.add(metadata);
+	}
+
+	public void add(String srcName, boolean moving, SourceType type) {
+
+		add(srcName, moving, type, null);
 	}
 
 	public void add(String srcName, boolean moving) {
@@ -181,6 +196,11 @@ public void add(String srcName) {
 		add(srcName, false);
 	}
 
+	public void add(String srcName, N5Metadata meta) {
+
+		add(srcName, false, SourceType.URL, meta);
+	}
+
 	public void addImagePlus(String srcName) {
 
 		addImagePlus(srcName, false);