Init ViewFromSourceAndConverterCreator

src/main/java/org/embl/mobie/viewer/source/LabelConverter.java → src/main/java/org/embl/mobie/viewer/color/LazyLabelConverter.java

@@ -26,7 +26,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package org.embl.mobie.viewer.source;
+package org.embl.mobie.viewer.color;
 
 import de.embl.cba.bdv.utils.lut.GlasbeyARGBLut;
 import de.embl.cba.tables.color.LazyCategoryColoringModel;
@@ -36,12 +36,12 @@
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.RealType;
 
-public class LabelConverter implements Converter<RealType<?>, ARGBType>, ColorConverter {
+public class LazyLabelConverter implements Converter<RealType<?>, ARGBType>, ColorConverter {
     private final LazyCategoryColoringModel<Double> coloringModel;
     private ARGBType singleColor;
     private double max = 500;
 
-    public LabelConverter() {
+    public LazyLabelConverter() {
         this.coloringModel = new LazyCategoryColoringModel<>(new GlasbeyARGBLut(255));
     }
 

src/main/java/org/embl/mobie/viewer/display/ImageSourceDisplay.java

@@ -10,6 +10,7 @@
 import sc.fiji.bdvpg.services.SourceAndConverterServices;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 public class ImageSourceDisplay extends AbstractSourceDisplay
@@ -77,28 +78,38 @@ public ImageSourceDisplay( ImageSourceDisplay imageDisplay )
 		this.sources.addAll( imageDisplay.sourceNameToSourceAndConverter.keySet() );
 
 		final SourceAndConverter< ? > sourceAndConverter = imageDisplay.sourceNameToSourceAndConverter.values().iterator().next();
+
+		setDisplaySettings( sourceAndConverter );
+
+		// TODO - show images in 3d (currently not supported in viewer)
+	}
+
+	public ImageSourceDisplay( SourceAndConverter< ? > sourceAndConverter )
+	{
+		sources = Arrays.asList( sourceAndConverter.getSpimSource().getName() );
+		setDisplaySettings( sourceAndConverter );
+	}
+
+	private void setDisplaySettings( SourceAndConverter< ? > sourceAndConverter )
+	{
 		final ConverterSetup converterSetup = SourceAndConverterServices.getSourceAndConverterService().getConverterSetup( sourceAndConverter );
 
 		if( sourceAndConverter.getConverter() instanceof AdjustableOpacityColorConverter )
 		{
-			this.opacity = ( ( AdjustableOpacityColorConverter ) sourceAndConverter.getConverter() ).getOpacity();
+			opacity = ( ( AdjustableOpacityColorConverter ) sourceAndConverter.getConverter() ).getOpacity();
 		}
 
 		if ( sourceAndConverter.getConverter() instanceof ColorConverter)
 		{
 			// needs to be of form r=(\\d+),g=(\\d+),b=(\\d+),a=(\\d+)"
-			String colorString = ( ( ColorConverter ) sourceAndConverter.getConverter() ).getColor().toString();
-			colorString = colorString.replaceAll("[()]", "");
-			this.color = colorString;
+			color = ( ( ColorConverter ) sourceAndConverter.getConverter() ).getColor().toString();
+			color = color.replaceAll("[()]", "");
 		}
 
-		double[] contrastLimits = new double[2];
+		contrastLimits = new double[2];
 		contrastLimits[0] = converterSetup.getDisplayRangeMin();
 		contrastLimits[1] = converterSetup.getDisplayRangeMax();
-		this.contrastLimits = contrastLimits;
-
-		this.blendingMode = (BlendingMode) SourceAndConverterServices.getSourceAndConverterService().getMetadata( sourceAndConverter, BlendingMode.BLENDING_MODE );
 
-		// TODO - show images in 3d (currently not supported in viewer)
+		blendingMode = (BlendingMode) SourceAndConverterServices.getSourceAndConverterService().getMetadata( sourceAndConverter, BlendingMode.BLENDING_MODE );
 	}
 }

src/main/java/org/embl/mobie/viewer/source/Sources.java

@@ -13,6 +13,7 @@
 import net.imglib2.util.Cast;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
+import org.embl.mobie.viewer.color.LazyLabelConverter;
 import org.scijava.ui.behaviour.ClickBehaviour;
 import org.scijava.ui.behaviour.io.InputTriggerConfig;
 import org.scijava.ui.behaviour.util.Behaviours;
@@ -28,7 +29,7 @@ public static <R extends NumericType<R> & RealType<R>> SourceAndConverter<R> rep
     }
 
     public static <R extends NumericType<R> & RealType<R>> BdvStackSource<?> showAsLabelMask(BdvStackSource<?> bdvStackSource) {
-        LabelConverter converter = new LabelConverter();
+        LazyLabelConverter converter = new LazyLabelConverter();
         SourceAndConverter<R> sac = replaceConverter(bdvStackSource.getSources().get(0), converter);
         BdvHandle bdvHandle = bdvStackSource.getBdvHandle();
         bdvStackSource.removeFromBdv();

src/main/java/org/embl/mobie/viewer/transform/AffineSourceTransformer.java

@@ -1,9 +1,12 @@
 package org.embl.mobie.viewer.transform;
 
+import bdv.tools.transformation.TransformedSource;
+import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
 import org.embl.mobie.viewer.playground.SourceAffineTransformer;
 import net.imglib2.realtransform.AffineTransform3D;
 
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -18,9 +21,25 @@ public class AffineSourceTransformer extends AbstractSourceTransformer
 	private transient AffineTransform3D affineTransform3D;
 
 	public AffineSourceTransformer( String name, double[] parameters, List< String > sources ) {
+		this( name, parameters, sources, null );
+	}
+
+	public AffineSourceTransformer( String name, double[] parameters, List< String > sources, List< String > sourceNamesAfterTransform )
+	{
 		this.name = name;
 		this.parameters = parameters;
 		this.sources = sources;
+		this.sourceNamesAfterTransform = sourceNamesAfterTransform;
+	}
+
+	public AffineSourceTransformer( TransformedSource< ? > transformedSource )
+	{
+		AffineTransform3D fixedTransform = new AffineTransform3D();
+		transformedSource.getFixedTransform( fixedTransform );
+		name = "manualTransform";
+		parameters = fixedTransform.getRowPackedCopy();
+		sources	= Arrays.asList( transformedSource.getWrappedSource().getName() );
+		sourceNamesAfterTransform =	Arrays.asList( transformedSource.getName() );
 	}
 
 	@Override

src/main/java/org/embl/mobie/viewer/view/ViewFromSourceAndConverterCreator.java

@@ -0,0 +1,132 @@
+package org.embl.mobie.viewer.view;
+
+import bdv.SpimSource;
+import bdv.tools.brightness.ConverterSetup;
+import bdv.tools.transformation.TransformedSource;
+import bdv.util.ResampledSource;
+import bdv.viewer.Source;
+import bdv.viewer.SourceAndConverter;
+import net.imglib2.converter.Converter;
+import net.imglib2.display.ColorConverter;
+import net.imglib2.realtransform.AffineTransform3D;
+import net.imglib2.type.numeric.ARGBType;
+import org.embl.mobie.viewer.bdv.render.BlendingMode;
+import org.embl.mobie.viewer.color.LabelConverter;
+import org.embl.mobie.viewer.color.OpacityAdjuster;
+import org.embl.mobie.viewer.display.ImageSourceDisplay;
+import org.embl.mobie.viewer.display.SourceDisplay;
+import org.embl.mobie.viewer.source.LabelSource;
+import org.embl.mobie.viewer.transform.AffineSourceTransformer;
+import org.embl.mobie.viewer.transform.MergedGridSource;
+import org.embl.mobie.viewer.transform.SourceTransformer;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class ViewFromSourceAndConverterCreator
+{
+	private final SourceAndConverter sourceAndConverter;
+
+	// display settings
+	private double opacity;
+	private BlendingMode blendingMode;
+	private double[] contrastLimits;
+	private String color;
+
+	public ViewFromSourceAndConverterCreator( SourceAndConverter sourceAndConverter )
+	{
+		this.sourceAndConverter = sourceAndConverter;
+	}
+
+	public View getView()
+	{
+		final ArrayList< SourceDisplay > sourceDisplays = new ArrayList<>();
+		final ArrayList< SourceTransformer > sourceTransformers = new ArrayList<>();
+		final View view = new View( "uiSelectionGroup", sourceDisplays, sourceTransformers, false );
+
+		// recursively add all transformations
+		// FIXME: in fact this will be the wrong order.
+		addSourceTransformers( sourceAndConverter.getSpimSource(), sourceTransformers );
+
+		if ( sourceAndConverter.getConverter() instanceof LabelConverter )
+		{
+			throwError( sourceAndConverter.getConverter() );
+		}
+		else
+		{
+			sourceDisplays.add( new ImageSourceDisplay( sourceAndConverter ) );
+		}
+
+		return view;
+	}
+
+	private void createSourceDisplay( SourceAndConverter< ? > sourceAndConverter  )
+	{
+		final Converter< ?, ARGBType > converter = sourceAndConverter.getConverter();
+		final ConverterSetup converterSetup = SourceAndConverterServices.getSourceAndConverterService().getConverterSetup( sourceAndConverter );
+
+		if( converter instanceof OpacityAdjuster )
+			opacity = ( ( OpacityAdjuster ) converter ).getOpacity();
+
+		if ( converter instanceof ColorConverter )
+		{
+			// needs to be of form r=(\\d+),g=(\\d+),b=(\\d+),a=(\\d+)"
+			color = ( ( ColorConverter ) converter ).getColor().toString();
+			color = color.replaceAll("[()]", "");
+		}
+
+		contrastLimits = new double[2];
+		contrastLimits[0] = converterSetup.getDisplayRangeMin();
+		contrastLimits[1] = converterSetup.getDisplayRangeMax();
+
+		blendingMode = (BlendingMode) SourceAndConverterServices.getSourceAndConverterService().getMetadata( sourceAndConverter, BlendingMode.BLENDING_MODE );
+	}
+
+	private void addSourceTransformers( Source< ? > source, List< SourceTransformer > sourceTransformers )
+	{
+		if ( source instanceof SpimSource )
+		{
+			return;
+		}
+		else if ( source instanceof TransformedSource )
+		{
+			final TransformedSource transformedSource = ( TransformedSource ) source;
+
+			AffineTransform3D fixedTransform = new AffineTransform3D();
+			transformedSource.getFixedTransform( fixedTransform );
+			if ( ! fixedTransform.isIdentity() )
+			{
+				sourceTransformers.add( new AffineSourceTransformer( transformedSource ) );
+			}
+
+			final Source< ? > wrappedSource = transformedSource.getWrappedSource();
+
+			addSourceTransformers( wrappedSource, sourceTransformers );
+		}
+		else if (  source instanceof LabelSource )
+		{
+			final Source< ? > wrappedSource = (( LabelSource ) source).getWrappedSource();
+
+			addSourceTransformers( wrappedSource, sourceTransformers );
+		}
+		else if (  source instanceof MergedGridSource )
+		{
+			throwError( source );
+		}
+		else if (  source instanceof ResampledSource )
+		{
+			throwError( source );
+		}
+		else
+		{
+			throwError( source );
+		}
+	}
+
+	private void throwError( Object object )
+	{
+		throw new UnsupportedOperationException( "Cannot yet create a view from a " + object.getClass().getName() );
+	}
+
+}

src/test/java/run/RunImageJ.java

@@ -1,12 +1,14 @@
 package run;
 
 import net.imagej.ImageJ;
+import org.scijava.command.CommandService;
 
 public class RunImageJ
 {
 	public static void main( String[] args )
 	{
-		final ImageJ imageJ = new ImageJ();
+		final ImageJ imageJ = new net.imagej.ImageJ();
 		imageJ.ui().showUI();
+		final CommandService command = imageJ.command();
 	}
 }