implemented workaround for ColorProcessor bug (pretty sure that's a b…

…ug) ...
saalfeldlab · Sep 25, 2024 · 36cc1db · 36cc1db
1 parent 9294a2c
commit 36cc1db
Showing 1 changed file with 22 additions and 14 deletions.
diff --git a/render-app/src/main/java/org/janelia/alignment/mapper/SingleChannelMapper.java b/render-app/src/main/java/org/janelia/alignment/mapper/SingleChannelMapper.java
@@ -15,7 +15,9 @@
 import net.imglib2.img.Img;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory;
+import net.imglib2.multithreading.SimpleMultiThreading;
 import net.imglib2.realtransform.AffineTransform2D;
+import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.view.Views;
 
@@ -32,6 +34,7 @@ public class SingleChannelMapper
 	final RealRandomAccess<UnsignedByteType> access;
 	final AffineTransform2D tInv;
 	final double[] tmp;
+	final boolean isRGB;
 
     // 2x2 subsampling using top-left pixels
     final int subsampling = 2;
@@ -44,7 +47,7 @@ public class SingleChannelMapper
 	// 3x3 subsampling using center pixels
 	//final int subsampling = 3;
 	//final long[] offset = new long[] { -1, -1 };
-
+ 
     public SingleChannelMapper(final ImageProcessorWithMasks source,
                                final ImageProcessorWithMasks target,
                                final boolean isMappingInterpolated) {
@@ -53,18 +56,19 @@ public SingleChannelMapper(final ImageProcessorWithMasks source,
         this.target = target;
         this.isMappingInterpolated = isMappingInterpolated;
 
+        this.isRGB = ColorProcessor.class.isInstance( normalizedSource.ip );
         if (isMappingInterpolated)
         {
             //this.normalizedSource.ip.setInterpolationMethod(ImageProcessor.BILINEAR);
-        	final Img<UnsignedByteType> img = ImageJFunctions.wrapByte( new ImagePlus( "", normalizedSource.ip ) );
-        	if ( img == null )
-        	{
-        		System.out.println( "normalizedSource.ip" + normalizedSource.ip );
-        		if ( normalizedSource.ip != null )
-        		System.out.println( "normalizedSource.ip class=" + normalizedSource.ip.getClass().getName() );
-        		System.out.println( "img=" + img );
-        		throw new RuntimeException( "Couldn't wrap normalizedSource.ip to imglib2 image." );
-        	}
+
+        	final Img<UnsignedByteType> img;
+
+        	// TODO: this is a bug, this should not be a ColorProcessor
+        	if ( isRGB )
+        		img = ImageJFunctions.wrapByte( new ImagePlus( "", normalizedSource.ip.convertToByte( false ) ) );
+        	else
+        		img = ImageJFunctions.wrapByte( new ImagePlus( "", normalizedSource.ip ) );
+
         	final RealRandomAccessible<UnsignedByteType> rra = createSubsampled( img, subsampling, offset );
         	this.access = rra.realRandomAccess();
 
@@ -79,9 +83,6 @@ public SingleChannelMapper(final ImageProcessorWithMasks source,
         	t.translate( shift );
 
         	this.tInv = t.inverse();
-
-        	//System.out.println( "t: " + t );
-        	//System.out.println( "tInv: " + tInv );
         }
         else
         {
@@ -162,7 +163,14 @@ public void mapInterpolated(final double sourceX,
     	tInv.apply( tmp, tmp );
     	access.setPosition( tmp );
 
-        target.ip.set(targetX, targetY, access.get().get() );
+
+    	if ( isRGB )
+    	{
+    		final int value = access.get().get();
+    		target.ip.set(targetX, targetY, ARGBType.rgba(value, value, value, 0) );
+    	}
+    	else
+    		target.ip.set(targetX, targetY, access.get().get() );
 
     	//ImageJFunctions.show( img );
     	//SimpleMultiThreading.threadHaltUnClean();