Let user also choose non-visible images for transformations, #1165

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.1.2</version>
+    <version>5.1.3-SNAPSHOT</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java

@@ -70,7 +70,8 @@ public abstract class AbstractTransformationCommand extends DynamicCommand imple
 //            style = "radioButtonHorizontal")
 //    public String selectedSourceName;
 
-    @Parameter ( label = "Moving image(s)", callback = "setMovingImages" )
+    // Note that this is populated by org.embl.mobie.command.widget.SwingSelectableImagesWidget
+    @Parameter ( label = "Moving image(s)" ) // , callback = "setMovingImages"
     public SelectableImages selectedImages = new SelectableImages();
 
     @Parameter ( label = "Transformed image(s) suffix",
@@ -133,7 +134,7 @@ protected void applyTransform( AffineTransform3D affineTransform3D )
         // https://imagesc.zulipchat.com/#narrow/stream/327238-Fiji/topic/Close.20Scijava.20Command.20UI
     }
 
-    protected void createAndSaveAffineTransformedImages(
+    protected static void createAndSaveAffineTransformedImages(
             Collection< Image< ? > > movingImages,
             AffineTransform3D affineTransform3D,
             String suffix )
@@ -164,7 +165,6 @@ protected void createAndSaveAffineTransformedImages(
         }
     }
 
-    // button callback => rename with care!
     protected void setMovingImages()
     {
 
@@ -220,7 +220,6 @@ protected void setMovingImages()
             AffineTransform3D initialTransform = new AffineTransform3D();
             movingSource.getFixedTransform( initialTransform );
             movingSourcesToInitialTransform.put( movingSource, initialTransform );
-
         }
     }
 

src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java

@@ -55,10 +55,10 @@ public class BigWarpRegistrationCommand extends AbstractRegistrationCommand impl
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-	@Parameter ( label = "Launch BigWarp", callback = "launchBigWarp")
+	@Parameter ( label = "Launch BigWarp", callback = "launchBigWarp" )
 	private Button launchBigWarp;
 
-	@Parameter ( label = "Apply current transform and exit", callback = "applyTransform")
+	@Parameter ( label = "Apply transform", callback = "applyTransform" )
 	private Button applyTransform;
 
 	private BigWarp< ? > bigWarp;
@@ -79,6 +79,8 @@ public void applyTransform()
 
 	public void launchBigWarp()
 	{
+		setMovingImages();
+
 		ISourceAndConverterService sacService = SourceAndConverterServices.getSourceAndConverterService();
 		SourceAndConverterBdvDisplayService bdvDisplayService = SourceAndConverterServices.getBdvDisplayService();
 

src/main/java/org/embl/mobie/command/context/EnterTransformationCommand.java

@@ -45,7 +45,7 @@ public class EnterTransformationCommand extends AbstractTransformationCommand
 	@Parameter ( label = "Transformation 3D affine" )
 	public String transformation = Arrays.toString( new AffineTransform3D().getRowPackedCopy() );
 
-	@Parameter ( label = "Apply", callback = "applyTransform" )
+	@Parameter ( label = "Apply transform", callback = "applyTransform" )
 	public Button applyTransform;
 
 
@@ -59,6 +59,8 @@ public class EnterTransformationCommand extends AbstractTransformationCommand
 
 	private void applyTransform()
 	{
+		setMovingImages();
+
 		AffineTransform3D affineTransform3D = new AffineTransform3D();
 		affineTransform3D.set( parseStringToDoubleArray( transformation ) );
 		applyTransform( affineTransform3D );

src/main/java/org/embl/mobie/command/context/FlipCommand.java

@@ -67,6 +67,8 @@ public void initialize()
 
 	public void applyTransform()
 	{
+		setMovingImages();
+
 		// FIXME: This needs a transform for each of the sacs
 		AffineTransform3D transform = createFlipTransform( movingSacs.iterator().next() );
 		applyTransform( transform );

src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java

@@ -41,7 +41,6 @@
 @Plugin(type = BdvPlaygroundActionCommand.class, attrs = {}, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - Manual")
 public class ManualTransformationCommand extends AbstractTransformationCommand
 {
-
 	public static final String INACTIVE = "Manual transform inactive";
 
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
@@ -69,6 +68,8 @@ public void initialize()
 
 	public void startManualTransform()
 	{
+		setMovingImages();
+
 		transformationEditor = new MoBIEManualTransformationEditor( bdvHandle.getViewerPanel(), bdvHandle.getKeybindings() );
 		transformationEditor.setTransformableSources( movingSacs );
 		transformationEditor.setActive( true );

src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java

@@ -69,8 +69,9 @@ public void set(final WidgetModel model) {
 		super.set(model);
 
 		BdvHandle bdvHandle = MoBIE.getInstance().getViewManager().getSliceViewer().getBdvHandle();
-		List< SourceAndConverter< ? > > visibleSacs = MoBIEHelper.getVisibleSacs( bdvHandle );
-		String[] names = visibleSacs.stream()
+
+		List< SourceAndConverter< ? > > sacs = MoBIEHelper.getSacs( bdvHandle ); //  MoBIEHelper.getVisibleSacs( bdvHandle );
+		String[] names = sacs.stream()
 				.map( sac -> sac.getSpimSource().getName() )
 				.collect( Collectors.toList() ).toArray( new String[ 0 ] );
 

src/main/java/org/embl/mobie/lib/MoBIEHelper.java

@@ -317,6 +317,12 @@ else if ( currentTimeMillis - lastLogMillis.get() > 6000 )
         return visibleSacs;
     }
 
+	public static List< SourceAndConverter< ? > > getSacs( BdvHandle bdv )
+	{
+		final SourceAndConverterBdvDisplayService displayService = SourceAndConverterServices.getBdvDisplayService();
+		return displayService.getSourceAndConverterOf( bdv );
+	}
+
     public static VoxelDimensions getPixelDimensions()
     {
         return new FinalVoxelDimensions( "pixel", 1.0, 1.0, 1.0 );