Merge pull request #1 from saalfeldlab/master

update paintera

README.md

@@ -41,6 +41,22 @@ java -Xmx16G -XX:+UseConcMarkSweepGC -jar target/paintera-0.1.0-SNAPSHOT-shaded.
 ```
 Replace `16G` with the maximum amount of memory that Paintera should use.
 
+#### Display help message and command line parameters
+```shell
+$ java -jar target/paintera-0.1.0-SNAPSHOT-shaded.jar --help
+Usage: Paintera [-h] [--height=HEIGHT] [--width=WIDTH]
+                [--label-source=LABEL_SOURCE]... [--raw-source=RAW_SOURCE]...
+      --height=HEIGHT   Initial height of viewer. Defaults to 600.
+      --label-source=LABEL_SOURCE
+                        Open label source at start-up. Has to be [file://]
+                          /path/to/<n5-or-hdf5>:path/to/dataset
+      --raw-source=RAW_SOURCE
+                        Open raw source at start-up. Has to be [file://]
+                          /path/to/<n5-or-hdf5>:path/to/dataset
+      --width=WIDTH     Initial width of viewer. Defaults to 800.
+  -h, --help            Display this help message.
+```
+
 ## Usage
 
 | Action | Description |

src/main/java/org/janelia/saalfeldlab/fx/ui/NumericSliderWithField.java

@@ -8,7 +8,6 @@
 
 public class NumericSliderWithField
 {
-
 	private final Slider slider;
 
 	private final TextField field;

src/main/java/org/janelia/saalfeldlab/paintera/Paintera.java

@@ -1,42 +1,35 @@
 package org.janelia.saalfeldlab.paintera;
 
+import java.io.IOException;
 import java.lang.invoke.MethodHandles;
 import java.util.Optional;
+import java.util.regex.Pattern;
 
 import org.janelia.saalfeldlab.fx.event.KeyTracker;
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews;
+import org.janelia.saalfeldlab.n5.N5Writer;
+import org.janelia.saalfeldlab.paintera.data.DataSource;
 import org.janelia.saalfeldlab.paintera.viewer3d.Viewer3DFX;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import bdv.viewer.ViewerOptions;
 import javafx.application.Application;
 import javafx.application.Platform;
+import javafx.geometry.Rectangle2D;
 import javafx.scene.Scene;
+import javafx.stage.Screen;
 import javafx.stage.Stage;
+import net.imglib2.Volatile;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
 import picocli.CommandLine;
 
 public class Paintera extends Application
 {
 
 	private static final Logger LOG = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
 
-	private final PainteraBaseView baseView = new PainteraBaseView(
-			Math.min( 8, Math.max( 1, Runtime.getRuntime().availableProcessors() / 2 ) ),
-			ViewerOptions.options().screenScales( new double[] { 1.0, 0.5, 0.25 } ),
-			si -> s -> si.getState( s ).interpolationProperty().get() );
-
-	private final OrthogonalViews< Viewer3DFX > orthoViews = baseView.orthogonalViews();
-
-	private final KeyTracker keyTracker = new KeyTracker();
-
-	final BorderPaneWithStatusBars paneWithStatus = new BorderPaneWithStatusBars(
-			baseView,
-			keyTracker );
-
-	final PainteraDefaultHandlers defaultHandlers = new PainteraDefaultHandlers( baseView, keyTracker, paneWithStatus );
-
-
 	@Override
 	public void start( final Stage stage ) throws Exception
 	{
@@ -49,17 +42,51 @@ public void start( final Stage stage ) throws Exception
 
 		if ( !parsedSuccessfully )
 		{
-			baseView.stop();
 			Platform.exit();
 			return;
 		}
 
+		int maxSize = 0;
+		for ( final Screen screen : Screen.getScreens() )
+		{
+			Rectangle2D bounds = screen.getVisualBounds();
+			maxSize = Math.max( ( int )bounds.getWidth(), maxSize );
+			maxSize = Math.max( ( int )bounds.getHeight(), maxSize );
+		}
+
+		LOG.debug( "max screen size = {}", maxSize );
+
+		final double[] screenScales = maxSize < 2500 ?
+				new double [] { 1.0 / 1.0, 1.0 / 2.0, 1.0 / 4.0, 1.0 / 8.0}:
+				new double [] { 1.0 / 2.0, 1.0 / 4.0, 1.0 / 8.0, 1.0 / 16.0};
+
+		final PainteraBaseView baseView = new PainteraBaseView(
+				Math.min( 8, Math.max( 1, Runtime.getRuntime().availableProcessors() / 2 ) ),
+				ViewerOptions.options().screenScales( screenScales ),
+				si -> s -> si.getState( s ).interpolationProperty().get() );
+
+		final OrthogonalViews< Viewer3DFX > orthoViews = baseView.orthogonalViews();
+
+		final KeyTracker keyTracker = new KeyTracker();
+
+		final BorderPaneWithStatusBars paneWithStatus = new BorderPaneWithStatusBars(
+				baseView,
+				keyTracker );
+
+		final PainteraDefaultHandlers defaultHandlers = new PainteraDefaultHandlers( baseView, keyTracker, paneWithStatus );
+
 		final Scene scene = new Scene( paneWithStatus.getPane() );
 		if ( LOG.isDebugEnabled() )
 		{
 			scene.focusOwnerProperty().addListener( ( obs, oldv, newv ) -> LOG.debug( "Focus changed: old={} new={}", oldv, newv ) );
 		}
 
+		for ( final String source : painteraArgs.rawSources() )
+			addRawFromString( baseView, source );
+
+		for ( final String source : painteraArgs.labelSources() )
+			addLabelFromString( baseView, source );
+
 		setFocusTraversable( orthoViews, false );
 
 		stage.setOnCloseRequest( event -> baseView.stop() );
@@ -86,4 +113,41 @@ private static void setFocusTraversable(
 		view.grid().getBottomRight().setFocusTraversable( isTraversable );
 	}
 
+	private static < D extends RealType< D > & NativeType< D >, T extends Volatile< D > & RealType< T > > Optional< DataSource< D, T > > addRawFromString(
+			final PainteraBaseView pbv,
+			final String identifier ) throws IOException
+	{
+		if ( !Pattern.matches( "^[a-z]+://.+", identifier ) )
+			return addRawFromString( pbv, "file://" + identifier );
+
+		if ( Pattern.matches( "^file://.+", identifier ) )
+		{
+			final String[] split = identifier.replaceFirst( "file://", "" ).split( ":" );
+			final N5Writer n5 = N5Helpers.n5Writer( split[ 0 ], 64, 64, 64 );
+			return pbv.addRawSource( n5, split[ 1 ] );
+		}
+
+		LOG.warn( "Unable to generate raw source from {}", identifier );
+		return Optional.empty();
+	}
+
+	private static void addLabelFromString( final PainteraBaseView pbv, final String identifier ) throws IOException
+	{
+		if ( !Pattern.matches( "^[a-z]+://.+", identifier ) )
+		{
+			addLabelFromString( pbv, "file://" + identifier );
+			return;
+		}
+
+		if ( Pattern.matches( "^file://.+", identifier ) )
+		{
+			final String[] split = identifier.replaceFirst( "file://", "" ).split( ":" );
+			final N5Writer n5 = N5Helpers.n5Writer( split[ 0 ], 64, 64, 64 );
+			final String dataset = split[ 1 ];
+			final double[] resolution = Optional.ofNullable( n5.getAttribute( dataset, "resolution", double[].class ) ).orElse( new double[] { 1.0, 1.0, 1.0 } );
+			final double[] offset = Optional.ofNullable( n5.getAttribute( dataset, "offset", double[].class ) ).orElse( new double[] { 0.0, 0.0, 0.0 } );
+			pbv.addLabelSource( n5, dataset, resolution, offset );
+		}
+	}
+
 }

src/main/java/org/janelia/saalfeldlab/paintera/PainteraBaseView.java

@@ -14,6 +14,8 @@
 import java.util.stream.Stream;
 
 import org.janelia.saalfeldlab.fx.ortho.OrthogonalViews;
+import org.janelia.saalfeldlab.n5.DataType;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.N5Writer;
 import org.janelia.saalfeldlab.paintera.composition.ARGBCompositeAlphaAdd;
@@ -39,7 +41,6 @@
 import org.janelia.saalfeldlab.paintera.state.GlobalTransformManager;
 import org.janelia.saalfeldlab.paintera.stream.HighlightingStreamConverter;
 import org.janelia.saalfeldlab.paintera.stream.ModalGoldenAngleSaturatedHighlightingARGBStream;
-import org.janelia.saalfeldlab.paintera.ui.opendialog.N5Helpers;
 import org.janelia.saalfeldlab.paintera.viewer3d.Viewer3DFX;
 import org.janelia.saalfeldlab.util.Colors;
 import org.janelia.saalfeldlab.util.HashWrapper;
@@ -53,6 +54,7 @@
 import bdv.viewer.SourceAndConverter;
 import bdv.viewer.ViewerOptions;
 import gnu.trove.set.hash.TLongHashSet;
+import javafx.beans.property.SimpleDoubleProperty;
 import javafx.beans.property.SimpleIntegerProperty;
 import javafx.collections.ListChangeListener;
 import javafx.collections.ObservableList;
@@ -162,6 +164,35 @@ public GlobalTransformManager manager()
 		return this.manager;
 	}
 
+	public < T extends RealType< T > & NativeType< T >, U extends Volatile< T > & RealType< U > > Optional< DataSource< T, U > > addRawSource(
+			final N5Reader n5,
+			final String dataset ) throws IOException
+	{
+		final DatasetAttributes attributes = n5.getDatasetAttributes(
+				N5Helpers.isMultiScale( n5, dataset )
+						? Paths.get( dataset, N5Helpers.listAndSortScaleDatasets( n5, dataset )[ 0 ] ).toString()
+						: dataset );
+		final DataType type = attributes.getDataType();
+		return addRawSource( n5, dataset, Color.WHITE, N5Helpers.minForType( type ), N5Helpers.maxForType( type ) );
+	}
+
+	public < T extends RealType< T > & NativeType< T >, U extends Volatile< T > & RealType< U > > Optional< DataSource< T, U > > addRawSource(
+			final N5Reader n5,
+			final String dataset,
+			final Color color,
+			final double min,
+			final double max ) throws IOException
+	{
+		return addRawSource(
+				n5,
+				dataset,
+				N5Helpers.getResolution( n5, dataset ),
+				N5Helpers.getOffset( n5, dataset ),
+				color,
+				min,
+				max );
+	}
+
 	public < T extends RealType< T > & NativeType< T >, U extends Volatile< T > & RealType< U > > Optional< DataSource< T, U > > addRawSource(
 			final N5Reader n5,
 			final String dataset,
@@ -227,6 +258,17 @@ public < T extends RealType< T >, U extends RealType< U > > void addRawSource(
 		}
 	}
 
+	public < D extends Type< D >, T extends Type< T > > Optional< DataSource< D, T > > addLabelSource(
+			final N5Writer n5,
+			final String dataset ) throws IOException
+	{
+		return addLabelSource(
+				n5,
+				dataset,
+				N5Helpers.getResolution( n5, dataset ),
+				N5Helpers.getOffset( n5, dataset ) );
+	}
+
 	public < D extends Type< D >, T extends Type< T > > Optional< DataSource< D, T > > addLabelSource(
 			final N5Writer n5,
 			final String dataset,
@@ -238,7 +280,7 @@ public < D extends Type< D >, T extends Type< T > > Optional< DataSource< D, T >
 
 		if ( !N5Helpers.isMultiScale( n5, dataset ) && !N5Helpers.isLabelMultisetType( n5, Paths.get( dataset, N5Helpers.listAndSortScaleDatasets( n5, dataset )[ 0 ] ).toString() ) )
 		{
-			LOG.debug( "Only multiscale label multisets supported at the moment. Not adding any data set" );
+			LOG.warn( "Only multiscale label multisets supported at the moment. Not adding any data set" );
 			return Optional.empty();
 		}
 
@@ -337,6 +379,8 @@ public < D extends Type< D >, T extends Type< T > > void addLabelSource(
 				viewer3D.meshesGroup(),
 				fragmentsInSelection,
 				new SimpleIntegerProperty(),
+				new SimpleDoubleProperty(),
+				new SimpleIntegerProperty(),
 				meshManagerExecutorService,
 				meshWorkerExecutorService );
 
@@ -514,7 +558,6 @@ public static double[][] scaleFactorsFromAffineTransforms( final Source< ? > sou
 			factors[ 2 ] = transform.get( 2, 2 ) / reference.get( 2, 2 );
 		}
 
-		if ( LOG.isDebugEnabled() )
 		{
 			LOG.debug( "Generated scaling factors:" );
 			Arrays.stream( scaleFactors ).map( Arrays::toString ).forEach( LOG::debug );

src/main/java/org/janelia/saalfeldlab/paintera/PainteraCommandLineArgs.java

@@ -2,25 +2,35 @@
 
 import java.util.concurrent.Callable;
 
+import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;
 
+@Command( name = "Paintera" )
 public class PainteraCommandLineArgs implements Callable< Boolean >
 {
 
-	@Option( names = { "--width" }, required = false, description = "Initial width of viewer. Defaults to 800." )
+	@Option( names = { "--width" }, paramLabel = "WIDTH", required = false, description = "Initial width of viewer. Defaults to 800." )
 	private int width = -1;
 
-	@Option( names = { "--height" }, required = false, description = "Initial height of viewer. Defaults to 600." )
+	@Option( names = { "--height" }, paramLabel = "HEIGHT", required = false, description = "Initial height of viewer. Defaults to 600." )
 	private int height = -1;
 
 	@Option( names = { "-h", "--help" }, usageHelp = true, description = "Display this help message." )
 	private boolean helpRequested;
 
+	@Option( names = { "--raw-source" }, paramLabel = "RAW_SOURCE", required = false, description = "Open raw source at start-up. Has to be [file://]/path/to/<n5-or-hdf5>:path/to/dataset" )
+	private String[] rawSources;
+
+	@Option( names = { "--label-source" }, paramLabel = "LABEL_SOURCE", required = false, description = "Open label source at start-up. Has to be [file://]/path/to/<n5-or-hdf5>:path/to/dataset" )
+	private String[] labelSources;
+
 	@Override
 	public Boolean call() throws Exception
 	{
 		width = width <= 0 ? 800 : width;
 		height = height <= 0 ? 600 : height;
+		rawSources = rawSources == null ? new String[] {} : rawSources;
+		labelSources = labelSources == null ? new String[] {} : labelSources;
 		return true;
 	}
 
@@ -34,4 +44,14 @@ public int height()
 		return height;
 	}
 
+	public String[] rawSources()
+	{
+		return rawSources.clone();
+	}
+
+	public String[] labelSources()
+	{
+		return labelSources.clone();
+	}
+
 }