diff --git a/pom.xml b/pom.xml
index 13a1e434..856a03f2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,7 +9,7 @@
org.embl.mobie
mobie-viewer-fiji
- 5.1.2
+ 5.1.3-SNAPSHOT
diff --git a/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java
index 6e6baf1f..8abd9c52 100644
--- a/src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java
+++ b/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 );
-
}
}
diff --git a/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java b/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java
index 511f9ea6..0386405d 100644
--- a/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java
+++ b/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();
diff --git a/src/main/java/org/embl/mobie/command/context/EnterTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/EnterTransformationCommand.java
index e9daffeb..e5ea1a28 100644
--- a/src/main/java/org/embl/mobie/command/context/EnterTransformationCommand.java
+++ b/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 );
diff --git a/src/main/java/org/embl/mobie/command/context/FlipCommand.java b/src/main/java/org/embl/mobie/command/context/FlipCommand.java
index 1a4423b9..68463cba 100644
--- a/src/main/java/org/embl/mobie/command/context/FlipCommand.java
+++ b/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 );
diff --git a/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java b/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
index 15714bdf..b7fb502d 100644
--- a/src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java
+++ b/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 );
diff --git a/src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java b/src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java
index 78d027bd..4b3739aa 100644
--- a/src/main/java/org/embl/mobie/command/widget/SwingSelectableImagesWidget.java
+++ b/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 ] );
diff --git a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
index f0c514b4..ed20523b 100644
--- a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
+++ b/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 );