Projection mode changer

readme.md

@@ -4,10 +4,10 @@ In this repository, we collect useful additions for the [BigDataViewer](https://
 ## List of actions
 * Read a source from disc
 * Add a source to a BDV
-* [Log the current mouse position](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdv/navigate/LogMousePositionDemo.java#L33)
-* [Log the current viewer transform](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdv/navigate/ViewTransformSetAndLogDemo.java#L35)
-* [Change the current viewer transform](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdv/navigate/ViewTransformSetAndLogDemo.java#L37-L40)
-* [Take a screenshot](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdv/screenshot/ScreenshotDemo.java)
+* [Log the current mouse position](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdvh/navigate/LogMousePositionDemo.java#L33)
+* [Log the current viewer transform](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdvh/navigate/ViewTransformSetAndLogDemo.java#L35)
+* [Change the current viewer transform](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdvh/navigate/ViewTransformSetAndLogDemo.java#L37-L40)
+* [Take a screenshot](https://github.com/haesleinhuepf/bigdataviewer-playground/blob/master/src/test/src/sc/fiji/bdvh/screenshot/ScreenshotDemo.java)
 
 ## Wishlist of actions
 Here we document actions we would like to have. If you know similar functionality in other repositories, feel free to contribute it here or send us a link where we can adopt code! Thanks :-)
@@ -19,7 +19,7 @@ Here we document actions we would like to have. If you know similar functionalit
 ## Coding guides
 We tried to follow these general guide lines:
 * Specific (atomic) functionality lives in a class implementing [Runnable](https://docs.oracle.com/javase/7/docs/api/java/lang/Runnable.html)
-  * The constructor takes a [BdvHandle](https://github.com/bigdataviewer/bigdataviewer-vistools/blob/master/src/main/java/bdv/util/BdvHandle.java) as parameter.
+  * The constructor takes a [BdvHandle](https://github.com/bigdataviewer/bigdataviewer-vistools/blob/master/src/main/java/bdvh/util/BdvHandle.java) as parameter.
   * More mandatory parameters for the functionality are handed over as additional constructor parameters.
   * Optional parameters are set with setter methods.
   * The `run()` method executes the concreate action.
@@ -35,7 +35,7 @@ Pseudo code example:
   }
 ```
 
-* Furthermore, [Demo code](https://github.com/haesleinhuepf/bigdataviewer-playground/tree/master/src/test/src/sc/fiji/bdv) in the test sources directory should demonstrate 
+* Furthermore, [Demo code](https://github.com/haesleinhuepf/bigdataviewer-playground/tree/master/src/test/src/sc/fiji/bdvh) in the test sources directory should demonstrate
   * the individual functionality, 
   * how to add it as key listeners to the BigDataViewer,
   * how to add it to the right-click menu of the BigDataViewer 

src/main/java/sc/fiji/bdvpg/bdv/ManualRegistrationStarter.java

@@ -6,7 +6,7 @@
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.ui.TransformListener;
 import org.scijava.vecmath.Point3d;
-import sc.fiji.bdvpg.services.BdvService;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
 import sc.fiji.bdvpg.sourceandconverter.transform.SourceAffineTransformer;
 
 import java.util.ArrayList;
@@ -77,17 +77,17 @@ public void run() {
         for (int i=0;i<sacs.length;i++) {
 
             // Wraps into a Transformed Source, if the source was displayed originally
-            if (BdvService.getSourceAndConverterDisplayService().getDisplaysOf(sacs[i]).contains(bdvHandle)) {
+            if (SourceAndConverterServices.getSourceAndConverterDisplayService().getDisplaysOf(sacs[i]).contains(bdvHandle)) {
                 displayedSacsWrapped.add(new SourceAffineTransformer(sacs[i], new AffineTransform3D()).getSourceOut());
                 originallyDisplayedSacs.add(sacs[i]);
             }
         }
 
         // Remove from display the originally dispalyed sources
-        BdvService.getSourceAndConverterDisplayService().remove(bdvHandle, originallyDisplayedSacs.toArray(new SourceAndConverter[originallyDisplayedSacs.size()]));
+        SourceAndConverterServices.getSourceAndConverterDisplayService().remove(bdvHandle, originallyDisplayedSacs.toArray(new SourceAndConverter[originallyDisplayedSacs.size()]));
 
         // Shows the displayed wrapped Source
-        BdvService.getSourceAndConverterDisplayService().show(bdvHandle, displayedSacsWrapped.toArray(new SourceAndConverter[displayedSacsWrapped.size()]));
+        SourceAndConverterServices.getSourceAndConverterDisplayService().show(bdvHandle, displayedSacsWrapped.toArray(new SourceAndConverter[displayedSacsWrapped.size()]));
 
         // View of the BdvHandle before starting the registration
         AffineTransform3D originalViewTransform = new AffineTransform3D();

src/main/java/sc/fiji/bdvpg/bdv/ManualRegistrationStopper.java

@@ -8,16 +8,17 @@
 import mpicbg.spim.data.registration.ViewTransform;
 import mpicbg.spim.data.registration.ViewTransformAffine;
 import net.imglib2.realtransform.AffineTransform3D;
-import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterService;
-import sc.fiji.bdvpg.services.BdvService;
+import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
+import sc.fiji.bdvpg.scijava.services.SourceAndConverterService;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
 import sc.fiji.bdvpg.sourceandconverter.transform.SourceAffineTransformer;
 
 import java.lang.reflect.Method;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.function.BiFunction;
 
-import static sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterService.SPIM_DATA_INFO;
+import static sc.fiji.bdvpg.scijava.services.SourceAndConverterService.SPIM_DATA_INFO;
 
 // TODO : Ensure volatile is working with source which are not AbstractSpimSource
 
@@ -95,19 +96,19 @@ public static SourceAndConverter mutateTransformedSourceAndConverter(AffineTrans
      * @return
      */
     public static SourceAndConverter mutateLastSpimdataTransformation(AffineTransform3D affineTransform3D, SourceAndConverter sac) {
-        assert BdvService
+        assert SourceAndConverterServices
                 .getSourceAndConverterService()
-                .getSourceAndConverterToMetadata().get(sac).containsKey(SPIM_DATA_INFO);
-        assert BdvService
+                .getSacToMetadata().get(sac).containsKey(SPIM_DATA_INFO);
+        assert SourceAndConverterServices
                 .getSourceAndConverterService()
-                .getSourceAndConverterToMetadata().get(sac).get(SPIM_DATA_INFO) instanceof BdvSourceAndConverterService.SpimDataInfo;
+                .getSacToMetadata().get(sac).get(SPIM_DATA_INFO) instanceof SourceAndConverterService.SpimDataInfo;
 
-        BdvSourceAndConverterService.SpimDataInfo sdi = ((BdvSourceAndConverterService.SpimDataInfo)
-                BdvService.getSourceAndConverterService()
-                        .getSourceAndConverterToMetadata().get(sac).get(SPIM_DATA_INFO));
+        SourceAndConverterService.SpimDataInfo sdi = ((SourceAndConverterService.SpimDataInfo)
+                SourceAndConverterServices.getSourceAndConverterService()
+                        .getSacToMetadata().get(sac).get(SPIM_DATA_INFO));
 
         // TODO : find a way to pass the ref of starter into this function ? but static looks great...
-        BdvHandle bdvHandle = BdvService.getSourceAndConverterDisplayService().getActiveBdv();
+        BdvHandle bdvHandle = SourceAndConverterServices.getSourceAndConverterDisplayService().getActiveBdv();
 
         int timePoint = bdvHandle.getViewerPanel().getState().getCurrentTimepoint();
 
@@ -153,19 +154,19 @@ public static SourceAndConverter mutateLastSpimdataTransformation(AffineTransfor
      * @return
      */
     public static SourceAndConverter appendNewSpimdataTransformation(AffineTransform3D affineTransform3D, SourceAndConverter sac) {
-        assert BdvService
+        assert SourceAndConverterServices
                 .getSourceAndConverterService()
-                .getSourceAndConverterToMetadata().get(sac).containsKey(SPIM_DATA_INFO);
-        assert BdvService
+                .getSacToMetadata().get(sac).containsKey(SPIM_DATA_INFO);
+        assert SourceAndConverterServices
                 .getSourceAndConverterService()
-                .getSourceAndConverterToMetadata().get(sac).get(SPIM_DATA_INFO) instanceof BdvSourceAndConverterService.SpimDataInfo;
+                .getSacToMetadata().get(sac).get(SPIM_DATA_INFO) instanceof SourceAndConverterService.SpimDataInfo;
 
-        BdvSourceAndConverterService.SpimDataInfo sdi = ((BdvSourceAndConverterService.SpimDataInfo)
-                BdvService.getSourceAndConverterService()
-                        .getSourceAndConverterToMetadata().get(sac).get(SPIM_DATA_INFO));
+        SourceAndConverterService.SpimDataInfo sdi = ((SourceAndConverterService.SpimDataInfo)
+                SourceAndConverterServices.getSourceAndConverterService()
+                        .getSacToMetadata().get(sac).get(SPIM_DATA_INFO));
 
-        // TODO : find a ref to starter
-        BdvHandle bdvHandle = BdvService.getSourceAndConverterDisplayService().getActiveBdv();
+        // TODO : find a way to pass the ref of starter into this function ? but static looks great...
+        BdvHandle bdvHandle = SourceAndConverterServices.getSourceAndConverterDisplayService().getActiveBdv();
 
         int timePoint = bdvHandle.getViewerPanel().getState().getCurrentTimepoint();
 
@@ -253,10 +254,10 @@ public void run() {
 
         // Removes temporary TransformedSourceAndConverter - in two times for performance issue
         List<SourceAndConverter> tempSacs = starter.getTransformedSourceAndConverterDisplayed();
-        BdvService.getSourceAndConverterDisplayService().remove(starter.bdvHandle,tempSacs.toArray(new SourceAndConverter[tempSacs.size()]));
+        SourceAndConverterServices.getSourceAndConverterDisplayService().remove(starter.bdvHandle,tempSacs.toArray(new SourceAndConverter[tempSacs.size()]));
 
         for (SourceAndConverter sac: tempSacs) {
-            BdvService.getSourceAndConverterService().remove(sac);
+            SourceAndConverterServices.getSourceAndConverterService().remove(sac);
         }
 
         int nSources = starter.getOriginalSourceAndConverter().length;
@@ -273,7 +274,7 @@ public void run() {
         }
 
         // Calls display ( array for performance issue )
-        BdvService.getSourceAndConverterDisplayService().show(starter.getBdvHandle(),
+        SourceAndConverterServices.getSourceAndConverterDisplayService().show(starter.getBdvHandle(),
                 transformedSacsToDisplay.toArray(new SourceAndConverter[transformedSacsToDisplay.size()]));
 
     }

src/main/java/sc/fiji/bdvpg/bdv/projector/AccumulateAverageProjectorARGB.java

@@ -55,8 +55,6 @@ protected void accumulate(
 		int aAvg = 0, rAvg = 0, gAvg = 0, bAvg = 0, n = 0;
 		int aAccu = 0, rAccu = 0, gAccu = 0, bAccu = 0;
 
-		int sourceIndex = 0;
-
 		for ( final Cursor< ? extends ARGBType > access : accesses )
 		{
 			final int value = access.get().get();

src/main/java/sc/fiji/bdvpg/bdv/projector/AccumulateMixedProjectorARGB.java

@@ -1,6 +1,6 @@
 package sc.fiji.bdvpg.bdv.projector;
 
-import bdv.tools.transformation.TransformedSource;
+import bdv.util.BdvHandle;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
 import bdv.viewer.render.AccumulateProjector;
@@ -10,39 +10,23 @@
 import net.imglib2.RandomAccessible;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.ARGBType;
-import sc.fiji.bdvpg.services.BdvService;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
 
 import java.util.ArrayList;
-import java.util.Map;
-import java.util.Set;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.concurrent.ExecutorService;
 
+import static sc.fiji.bdvpg.bdv.projector.Projection.PROJECTION_MODE;
+import static sc.fiji.bdvpg.bdv.projector.Projection.PROJECTION_MODE_SUM;
+
 public class AccumulateMixedProjectorARGB extends AccumulateProjector< ARGBType, ARGBType >
 {
-	public static AccumulateProjectorFactory< ARGBType > factory = new AccumulateProjectorFactory< ARGBType >()
-	{
-		@Override
-		public AccumulateMixedProjectorARGB createAccumulateProjector(
-				final ArrayList< VolatileProjector > sourceProjectors,
-				final ArrayList< Source< ? > > sources,
-				final ArrayList< ? extends RandomAccessible< ? extends ARGBType > > sourceScreenImages,
-				final RandomAccessibleInterval< ARGBType > targetScreenImage,
-				final int numThreads,
-				final ExecutorService executorService )
-		{
-			return new AccumulateMixedProjectorARGB(
-					sourceProjectors,
-					sources,
-					sourceScreenImages,
-					targetScreenImage,
-					numThreads,
-					executorService );
-		}
-	};
-
-	private final ArrayList< Source< ? > > sourceList;
+	private final String[] projectionModes;
 
 	public AccumulateMixedProjectorARGB(
+			BdvHandle bdvHandle,
 			final ArrayList< VolatileProjector > sourceProjectors,
 			final ArrayList< Source< ? > > sources,
 			final ArrayList< ? extends RandomAccessible< ? extends ARGBType > > sourceScreenImages,
@@ -51,7 +35,7 @@ public AccumulateMixedProjectorARGB(
 			final ExecutorService executorService )
 	{
 		super( sourceProjectors, sourceScreenImages, target, numThreads, executorService );
-		this.sourceList = sources;
+		this.projectionModes = getProjectionModes( bdvHandle, sources );
 	}
 
 	@Override
@@ -64,8 +48,6 @@ protected void accumulate(
 
 		int sourceIndex = 0;
 
-		final Map< SourceAndConverter, Map< String, Object > > sourceAndConverterToMetadata = BdvService.getSourceAndConverterService().getSourceAndConverterToMetadata();
-
 		for ( final Cursor< ? extends ARGBType > access : accesses )
 		{
 			final int value = access.get().get();
@@ -79,16 +61,14 @@ protected void accumulate(
 				continue;
 			}
 
-			String projectionMode = getProjectionMode( sourceIndex, sourceAndConverterToMetadata );
-
-			if ( projectionMode.equals( Projection.PROJECTION_MODE_SUM ) )
+			if ( projectionModes[sourceIndex] == ( Projection.PROJECTION_MODE_SUM ) )
 			{
 				aAccu += a;
 				rAccu += r;
 				gAccu += g;
 				bAccu += b;
 			}
-			else if ( projectionMode.equals( Projection.PROJECTION_MODE_AVG ))
+			else if ( projectionModes[sourceIndex] == ( Projection.PROJECTION_MODE_AVG ))
 			{
 				aAvg += a;
 				rAvg += r;
@@ -126,26 +106,44 @@ else if ( projectionMode.equals( Projection.PROJECTION_MODE_AVG ))
 
 	}
 
-	private String getProjectionMode( int sourceIndex, Map< SourceAndConverter, Map< String, Object > > sourceAndConverterToMetadata )
+	private String[] getProjectionModes( BdvHandle bdvHandle, ArrayList< Source< ? > > sources )
 	{
-		Source< ? > source = sourceList.get( sourceIndex );
-		if ( source instanceof TransformedSource )
-			source = (( TransformedSource )source).getWrappedSource();
+		// We need to reconstitute the sequence of action that lead to the current indexes
+
+		// Getting the sources present in the BdvHandle
+		List<SourceAndConverter> sacsInBdvHandle = SourceAndConverterServices
+				.getSourceAndConverterDisplayService()
+				.getSourceAndConverterOf(bdvHandle);
+
+		// Fetching the indexes of visible sources in the BdvHandle
+		List<Integer> visibleIndexes = bdvHandle.getViewerPanel().getState().getVisibleSourceIndices();
+		// In ascending order
+		Collections.sort(visibleIndexes);
+
+		SourceAndConverter[] sacArray = new SourceAndConverter[visibleIndexes.size()];
 
-		String projectionMode = "Sum";
+		for (int idx = 0; idx<visibleIndexes.size(); idx++) {
+			sacArray[idx] = sacsInBdvHandle.get(visibleIndexes.get(idx));
+		}
+
+		final List< SourceAndConverter > sacs = Arrays.asList(sacArray);//SourceAndConverterServices.getSourceAndConverterService().getSourceAndConverters();
+		final String[] projectionModes = new String[ sources.size() ];
 
-		for ( SourceAndConverter sac : sourceAndConverterToMetadata.keySet() )
+		int sourceIndex = 0;
+
+		for ( SourceAndConverter<?> sac : sacs )
 		{
-			if ( sac.getSpimSource().equals( source ) )
-			{
-				final Set< String > metadata = sourceAndConverterToMetadata.get( sac ).keySet();
-				if ( metadata.contains( Projection.PROJECTION_MODE ) )
-				{
-					projectionMode = (String) sourceAndConverterToMetadata.get( sac ).get( Projection.PROJECTION_MODE );
-				}
-			}
+
+			final String projectionMode = (String) SourceAndConverterServices.getSourceAndConverterService().getMetadata( sac, PROJECTION_MODE );
+
+			if ( projectionMode == null )
+				projectionModes[sourceIndex++] = PROJECTION_MODE_SUM;
+			else
+				projectionModes[sourceIndex++] = projectionMode;
+
 		}
-		return projectionMode;
+
+		return projectionModes;
 	}
 
 }

src/main/java/sc/fiji/bdvpg/bdv/projector/AccumulateMixedProjectorARGBFactory.java

@@ -0,0 +1,46 @@
+package sc.fiji.bdvpg.bdv.projector;
+
+import bdv.util.Bdv;
+import bdv.util.BdvHandle;
+import bdv.viewer.Source;
+import bdv.viewer.render.AccumulateProjectorFactory;
+import bdv.viewer.render.VolatileProjector;
+import net.imglib2.RandomAccessible;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.numeric.ARGBType;
+
+import java.util.ArrayList;
+import java.util.concurrent.ExecutorService;
+
+public class AccumulateMixedProjectorARGBFactory implements AccumulateProjectorFactory< ARGBType >
+{
+	private BdvHandle bdvHandle;
+
+	public AccumulateMixedProjectorARGBFactory()
+	{
+	}
+
+	public void setBdvHandle( BdvHandle bdvHandle )
+	{
+		this.bdvHandle = bdvHandle;
+	}
+
+	@Override
+	public VolatileProjector createAccumulateProjector(
+			ArrayList< VolatileProjector > sourceProjectors,
+			ArrayList< Source< ? > > sources,
+			ArrayList< ? extends RandomAccessible< ? extends ARGBType > > sourceScreenImages,
+			RandomAccessibleInterval< ARGBType > targetScreenImage,
+			int numThreads,
+			ExecutorService executorService )
+	{
+		return new AccumulateMixedProjectorARGB(
+						bdvHandle,
+						sourceProjectors,
+						sources,
+						sourceScreenImages,
+						targetScreenImage,
+						numThreads,
+						executorService );
+	}
+}

src/main/java/sc/fiji/bdvpg/bdv/sourceandconverter/SourceAdder.java

@@ -2,7 +2,7 @@
 
 import bdv.util.BdvHandle;
 import bdv.viewer.SourceAndConverter;
-import sc.fiji.bdvpg.services.BdvService;
+import sc.fiji.bdvpg.services.SourceAndConverterServices;
 
 import java.util.function.Consumer;
 
@@ -22,6 +22,6 @@ public void run() {
 
 	@Override
 	public void accept(SourceAndConverter source) {
-		BdvService.getSourceAndConverterDisplayService().show(bdvh, source);
+		SourceAndConverterServices.getSourceAndConverterDisplayService().show(bdvh, source);
 	}
 }