Add ROIs to ScreenShotMaker

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

@@ -35,7 +35,11 @@
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
+import ij.gui.Roi;
+import ij.plugin.filter.ThresholdToSelection;
+import ij.process.ByteProcessor;
 import ij.process.ImageConverter;
+import ij.process.ImageProcessor;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.lib.MoBIEHelper;
@@ -51,6 +55,7 @@
 import sc.fiji.bdvpg.bdv.BdvHandleHelper;
 import sc.fiji.bdvpg.scijava.command.BdvPlaygroundActionCommand;
 
+import java.awt.*;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
@@ -75,9 +80,6 @@ public class AutomaticRegistrationCommand extends DynamicCommand implements BdvP
 	@Parameter(label="Registration Voxel Size", persist = false, min = "0.0", style="format:#.00000")
 	public Double voxelSize = 1D;
 
-	@Parameter(label="Out of Bounds Value")
-	public String outOfBoundsValue = "Do not use";
-
 	@Parameter ( label = "Transformation", choices = { TRANSLATION, RIGID, SIMILARITY, AFFINE } )
 	private String transformationType = TRANSLATION;
 
@@ -153,15 +155,7 @@ private void compute()
 		// create two 2D ImagePlus that are to be aligned
 		//
 		ScreenShotMaker screenShotMaker = new ScreenShotMaker( bdvHandle, sacA.getSpimSource().getVoxelDimensions().unit() );
-		try
-		{
-			// useful for images with bright background
-			// to avoid an edge with the black background of BDV
-			screenShotMaker.setOutOfBoundsValue( Float.parseFloat( this.outOfBoundsValue ) );
-		} catch ( Exception e )
-		{
-			// don't set an out-of-bounds value.
-		}
+
 		screenShotMaker.run( Arrays.asList( sacA, sacB ), voxelSize );
 		CompositeImage compositeImage = screenShotMaker.getCompositeImagePlus();
 		AffineTransform3D canvasToGlobalTransform = screenShotMaker.getCanvasToGlobalTransform();
@@ -170,16 +164,21 @@ private void compute()
 		ImagePlus impA = new ImagePlus( imageA + " (fixed)", stack.getProcessor( 1 ) );
 		ImagePlus impB = new ImagePlus( imageB + " (moving)", stack.getProcessor( 2 ) );
 
-		// set the display ranges and burn them in by converting to unit8
+		// set the display ranges and burn them in by converting to uint8
 		// this is important for the intensity based registration methods
 		compositeImage.setPosition( 1 );
 		impA.getProcessor().setMinAndMax( compositeImage.getDisplayRangeMin(), compositeImage.getDisplayRangeMax() );
+		new ImageConverter( impA ).convertToGray8();
+
 		compositeImage.setPosition( 2 );
 		impB.getProcessor().setMinAndMax( compositeImage.getDisplayRangeMin(), compositeImage.getDisplayRangeMax() );
-		new ImageConverter( impA ).convertToGray8();
 		new ImageConverter( impB ).convertToGray8();
-		double min = impA.getProcessor().getMax();
-		double max = impA.getProcessor().getMax();
+
+		// set the rois within which the images contain valid pixel values
+		// those are used by some registration methods, e.g. turboReg
+		Roi[] rois = screenShotMaker.getMasks();
+		impA.setRoi( rois[ 0 ] );
+		impB.setRoi( rois[ 1 ] );
 
 		// compute the transformation that aligns the two images in 2D
 		//

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

@@ -30,6 +30,8 @@
 
 import bdv.util.BdvHandle;
 import ij.IJ;
+import ij.gui.Roi;
+import ij.plugin.frame.RoiManager;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.command.CommandConstants;
 import org.embl.mobie.lib.bdv.ScreenShotMaker;
@@ -63,13 +65,13 @@ public class ScreenShotMakerCommand extends DynamicCommand implements BdvPlaygro
     @Override
     public void run()
     {
+        if ( MoBIE.getInstance().getSettings().values.isOpenedFromCLI() )
+            MoBIE.imageJ.ui().showUI();
+
         ScreenShotMaker screenShotMaker = new ScreenShotMaker( bdvHandle, pixelUnit );
         screenShotMaker.run( targetSamplingInXY );
         screenShotMaker.getRGBImagePlus().show();
         screenShotMaker.getCompositeImagePlus().show();
-
-        if ( MoBIE.getInstance().getSettings().values.isOpenedFromCLI() )
-            MoBIE.imageJ.ui().showUI();
     }
 
     @Override
@@ -99,7 +101,5 @@ private void showNumPixels()
     {
         final long[] sizeInPixels = ScreenShotMaker.getCaptureImageSizeInPixels( bdvHandle, targetSamplingInXY );
         IJ.log( CAPTURE_SIZE_PIXELS + Arrays.toString( sizeInPixels ) );
-//        final MutableModuleItem< String > message = getInfo().getMutableInput("message", String.class);
-//        message.setValue( this, CAPTURE_SIZE_PIXELS + sizeInPixels[ 0 ] + ", " + sizeInPixels[ 1 ] );
     }
 }

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

@@ -157,8 +157,9 @@ else if ( mode.equals( AdditionMode.Concatenate ) )
 		}
 	}
 
-	public static double[] parseStringToDoubleArray(String arrayStr) {
-		arrayStr = arrayStr.replaceAll("[^0-9.,]", "");
+	public static double[] parseStringToDoubleArray(String arrayStr)
+	{
+		arrayStr = arrayStr.replaceAll("\\[|\\]", "");
 		String[] items = arrayStr.split(",\\s*");
 		double[] doubles = Arrays.stream(items).mapToDouble(Double::parseDouble).toArray();
 		return doubles;

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

@@ -61,7 +61,7 @@
 import java.util.Optional;
 import java.util.Set;
 
-@Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Show " + ShowRasterImagesCommand.RAW + " Image(s)" )
+@Plugin(type = BdvPlaygroundActionCommand.class, menuPath = CommandConstants.CONTEXT_MENU_ITEMS_ROOT + "Show " + ShowRasterImagesCommand.RAW + " Images" )
 public class ShowRasterImagesCommand< T extends NumericType< T > > implements BdvPlaygroundActionCommand
 {
 	static { net.imagej.patcher.LegacyInjector.preinit(); }

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

@@ -55,8 +55,6 @@ public class SourcesInfoCommand implements BdvPlaygroundActionCommand
 {
     static { net.imagej.patcher.LegacyInjector.preinit(); }
 
-    public static final String CAPTURE_SIZE_PIXELS = "Capture size [pixels]: ";
-
     @Parameter
     public BdvHandle bdvHandle;
 
@@ -68,16 +66,18 @@ public void run()
         {
             Source< ? > source = sac.getSpimSource();
             IJ.log( "# " + source.getName() );
+            IJ.log( "Data type: " + source.getType().getClass() );
+            IJ.log( "Shape: " + Arrays.toString( source.getSource( 0,0 ).dimensionsAsLongArray() ) );
             IJ.log( "Number of resolution levels: " + source.getNumMipmapLevels() );
             IJ.log( "Voxel size: " + Arrays.toString( source.getVoxelDimensions().dimensionsAsDoubleArray() ) );
 
             if ( source instanceof TransformedSource )
             {
                 AffineTransform3D transform3D = new AffineTransform3D();
                 ( ( TransformedSource<?> ) source ).getFixedTransform( transform3D );
-                IJ.log( "Additional transform: " + transform3D );
+                IJ.log( "Additional transform:\n" + Arrays.toString( transform3D.getRowPackedCopy() ) );
                 source.getSourceTransform( 0, 0, transform3D );
-                IJ.log( "Full transform: " + transform3D );
+                IJ.log( "Full transform:\n" + Arrays.toString( transform3D.getRowPackedCopy() ) );
             }
         });
     }