Improve SIFT Dialog

mobie · Dec 28, 2023 · 65197bc · 65197bc
1 parent f69f0b8
commit 65197bc
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Showing 4 changed files with 68 additions and 33 deletions.
diff --git a/src/main/java/org/embl/mobie/command/context/SIFT2DAlignCommand.java b/src/main/java/org/embl/mobie/command/context/SIFT2DAlignCommand.java
@@ -32,24 +32,61 @@
 import bdv.util.BdvHandle;
 import bdv.viewer.SourceAndConverter;
 import ij.IJ;
-import ij.gui.NonBlockingGenericDialog;
-import ij.gui.YesNoCancelDialog;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.command.CommandConstants;
+import org.scijava.command.Interactive;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
+import org.scijava.widget.Button;
 import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand;
 
 @Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Transform>Registration - SIFT")
-public class SIFT2DAlignCommand implements BdvPlaygroundActionCommand
+public class SIFT2DAlignCommand implements BdvPlaygroundActionCommand, Interactive
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
 	@Parameter
 	public BdvHandle bdvHandle;
 
+	@Parameter ( label = "Compute Alignment", callback = "compute")
+	private Button compute;
+
+	@Parameter ( label = "Toggle Alignment", callback = "toggle")
+	private Button toggle;
+
+	private AffineTransform3D previousTransform;
+	private AffineTransform3D newTransform;
+	private TransformedSource< ? > transformedSource;
+	private boolean isAligned;
+
 	@Override
 	public void run()
+	{
+		//
+	}
+
+	private void toggle()
+	{
+		if ( transformedSource == null )
+		{
+			IJ.showMessage( "Please first [ Compute Alignment ]." );
+			return;
+		}
+
+		if ( isAligned )
+		{
+			transformedSource.setFixedTransform( previousTransform );
+		}
+		else
+		{
+			transformedSource.setFixedTransform( newTransform );
+		}
+
+		bdvHandle.getViewerPanel().requestRepaint();
+		isAligned = ! isAligned;
+	}
+
+	private void compute()
 	{
 		IJ.log("# SIFT registration" +
 				"\nThe registration is computed in the currently visible 2D plane" +
@@ -63,33 +100,26 @@ public void run()
 		if ( movingSac.getSpimSource() instanceof TransformedSource )
 		{
 			// apply the transformation
-			AffineTransform3D siftTransform3D = aligner.getSiftTransform3D();
-			TransformedSource< ? > transformedSource = ( TransformedSource< ? > ) movingSac.getSpimSource();
-			AffineTransform3D previousFixedTransform = new AffineTransform3D();
-			transformedSource.getFixedTransform( previousFixedTransform );
-			AffineTransform3D newFixedTransform = previousFixedTransform.copy();
-			newFixedTransform.preConcatenate( siftTransform3D );
-			transformedSource.setFixedTransform( newFixedTransform );
-			bdvHandle.getViewerPanel().requestRepaint();
+			AffineTransform3D siftTransform = aligner.getSiftTransform3D();
+			transformedSource = ( TransformedSource< ? > ) movingSac.getSpimSource();
+			previousTransform = new AffineTransform3D();
+			transformedSource.getFixedTransform( previousTransform );
+			newTransform = previousTransform.copy();
+			newTransform.preConcatenate( siftTransform );
+			transformedSource.setFixedTransform( newTransform );
+			IJ.showMessage( "Transforming " + transformedSource.getName() );
+			IJ.showMessage( "Previous Transform: " + previousTransform );
+			IJ.showMessage( "Additional SIFT Transform: " + siftTransform );
+			IJ.showMessage( "Combined Transform: " + newTransform );
 
-			// ask user whether to accept the transformation
-			NonBlockingGenericDialog dialog = new NonBlockingGenericDialog( "SIFT Alignment" );
-			dialog.addMessage( "Press OK to keep the transformation" );
-			dialog.addMessage( "Press Cancel to discard the transformation" );
-			dialog.showDialog();
-			if ( dialog.wasOKed() )
-			{
-				IJ.log( "Transformed " + movingSac.getSpimSource().getName() + " with " + siftTransform3D );
-			}
-			else if ( dialog.wasCanceled() )
-			{
-				transformedSource.setFixedTransform( previousFixedTransform );
-				bdvHandle.getViewerPanel().requestRepaint();
-			}
+			isAligned = true;
+			bdvHandle.getViewerPanel().requestRepaint();
 		}
 		else
 		{
 			IJ.log("Cannot apply transformation to image of type " + movingSac.getSpimSource().getClass() );
 		}
 	}
+
+
 }
diff --git a/src/main/java/org/embl/mobie/command/context/SIFT2DAligner.java b/src/main/java/org/embl/mobie/command/context/SIFT2DAligner.java
@@ -79,6 +79,8 @@ public class SIFT2DAligner
     private SourceAndConverter< ? > fixedSac;
     private SourceAndConverter< ? > movingSac;
     private ScreenShotMaker screenShotMaker;
+    private static String fixedImageName;
+    private static String movingImageName;
 
     static private class Param
     {
@@ -135,8 +137,9 @@ public SIFT2DAligner( BdvHandle bdvHandle )
 
     public boolean showUI()
     {
-        if( p.pixelSize == null )
-            p.pixelSize = BdvHandleHelper.getViewerVoxelSpacing( bdvHandle );
+        double viewerVoxelSpacing = BdvHandleHelper.getViewerVoxelSpacing( bdvHandle );
+
+        p.pixelSize = 2 * viewerVoxelSpacing;
 
         List< SourceAndConverter< ? > > sourceAndConverters = MoBIEHelper.getVisibleSacs( bdvHandle );
         if ( sourceAndConverters.size() < 2 )
@@ -151,8 +154,11 @@ public boolean showUI()
 
         final GenericDialog gd = new GenericDialog( "SIFT 2D Aligner" );
 
-        gd.addChoice( "fixed_image :", titles, titles[ 0 ] );
-        gd.addChoice( "moving_image :", titles, titles[ 1 ] );
+        String fixedDefault = Arrays.asList( titles ).contains( fixedImageName ) ? fixedImageName : titles[ 0 ];
+        gd.addChoice( "fixed_image :", titles, fixedDefault );
+
+        String movingDefault = Arrays.asList( titles ).contains( movingImageName ) ? movingImageName : titles[ 1 ];
+        gd.addChoice( "moving_image :", titles, movingDefault );
         String voxelUnit = sourceAndConverters.get( 0 ).getSpimSource().getVoxelDimensions().unit();
 
         gd.addNumericField( "pixel_size :", p.pixelSize, 2, 6, voxelUnit );
@@ -178,8 +184,8 @@ public boolean showUI()
 
         if (gd.wasCanceled()) return false;
 
-        String fixedImageName = gd.getNextChoice();
-        String movingImageName = gd.getNextChoice();
+        fixedImageName = gd.getNextChoice();
+        movingImageName = gd.getNextChoice();
 
         p.pixelSize = gd.getNextNumber();
         p.modelIndex = gd.getNextChoiceIndex();

diff --git a/src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java b/src/main/java/org/embl/mobie/command/open/OpenHCSDatasetCommand.java
@@ -37,7 +37,6 @@
 import org.scijava.plugin.Plugin;
 import org.scijava.widget.Button;
 
-import java.io.File;
 import java.io.IOException;
 
 

diff --git a/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java b/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java
@@ -10,7 +10,7 @@ public class OpenEMXRAY
 {
     public static void main( String[] args ) throws IOException
     {
-        OpenerLogging.setLogging( true );
+//        OpenerLogging.setLogging( true );
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
         new MoBIE("/Volumes/cba/exchange/em-xray-alignment/mobie" );