From 9e87d5a6bb6b8f8b11540406284e59f21953756a Mon Sep 17 00:00:00 2001
From: Stephan Saalfeld <saalfeld@mpi-cbg.de>
Date: Tue, 17 Aug 2010 00:12:39 +0200
Subject: [PATCH] Fixed bug 202

http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=202
---
 ini/trakem2/display/Display.java          |  2 +-
 mpicbg/trakem2/align/AlignLayersTask.java | 36 ++++++++++++++++++++-----------
 2 files changed, 24 insertions(+), 14 deletions(-)

diff --git a/ini/trakem2/display/Display.java b/ini/trakem2/display/Display.java
index 63185da1..8977bd59 100644
--- a/ini/trakem2/display/Display.java
+++ b/ini/trakem2/display/Display.java
@@ -3803,7 +3803,7 @@ public final class Display extends DBObject implements ActionListener, IJEventLi
 		} else if (command.equals("Apply transform propagating to last layer")) {
 			if (mode.getClass() == AffineTransformMode.class || mode.getClass() == NonLinearTransformMode.class) {
 				final LayerSet ls = getLayerSet();
-				final HashSet<Layer> subset = new HashSet<Layer>(ls.getLayers(ls.indexOf(Display.this.layer)+1, ls.size())); // +1 to exclude current layer
+				final HashSet<Layer> subset = new HashSet<Layer>(ls.getLayers(ls.indexOf(Display.this.layer)+1, ls.size()-1)); // +1 to exclude current layer
 				if (mode.getClass() == AffineTransformMode.class) ((AffineTransformMode)mode).applyAndPropagate(subset);
 				else if (mode.getClass() == NonLinearTransformMode.class) ((NonLinearTransformMode)mode).apply(subset);
 				setMode(new DefaultMode(Display.this));
diff --git a/mpicbg/trakem2/align/AlignLayersTask.java b/mpicbg/trakem2/align/AlignLayersTask.java
index 7af0667c..6c7d8f37 100644
--- a/mpicbg/trakem2/align/AlignLayersTask.java
+++ b/mpicbg/trakem2/align/AlignLayersTask.java
@@ -23,6 +23,7 @@ import ij.process.ImageProcessor;
 import ini.trakem2.display.Display;
 import ini.trakem2.display.Displayable;
 import ini.trakem2.display.Layer;
+import ini.trakem2.display.LayerSet;
 import ini.trakem2.display.Patch;
 import ini.trakem2.persistence.Loader;
 import ini.trakem2.utils.Bureaucrat;
@@ -138,13 +139,7 @@ final public class AlignLayersTask
 				if (index < cstart.getSelectedIndex()) cstart.select(index);
 				if (index < cref.getSelectedIndex()) cref.select(index);
 			}
-		});		
-
-		Align.param.addFields( gd );
-		gd.addCheckbox( "use bUnwarpJ (non-linear cubic B-Splines)", useBUnwarpJ );
-		
-		gd.addMessage( "Miscellaneous:" );
-		gd.addCheckbox( "propagate after last transform", propagateTransform );
+		});
 		
 		gd.showDialog();
 		if ( gd.wasCanceled() ) return;
@@ -152,11 +147,22 @@ final public class AlignLayersTask
 		final int first = gd.getNextChoiceIndex();
 		final int ref = gd.getNextChoiceIndex();
 		final int last = gd.getNextChoiceIndex();
+
+		final GenericDialog gd2 = new GenericDialog( "Align Layers" );
+		
+		Align.param.addFields( gd2 );
+		gd2.addCheckbox( "use bUnwarpJ (non-linear cubic B-Splines)", useBUnwarpJ );
 		
-		Align.param.readFields( gd );
+		gd2.addMessage( "Miscellaneous:" );
+		gd2.addCheckbox( "propagate after last transform", propagateTransform );
 		
-		useBUnwarpJ = gd.getNextBoolean();
-		propagateTransform = gd.getNextBoolean();
+		gd2.showDialog();
+		if ( gd2.wasCanceled() ) return;
+		
+		Align.param.readFields( gd2 );
+		
+		useBUnwarpJ = gd2.getNextBoolean();
+		propagateTransform = gd2.getNextBoolean();
 		
 		if (useBUnwarpJ && !elasticParam.showDialog()) return;
 
@@ -334,9 +340,13 @@ final public class AlignLayersTask
 		}
 		if ( propagateTransform )
 		{
-			for (Layer la : l.getParent().getLayers(last > first ? last +1 : first -1, last > first ? l.getParent().size() -1 : 0)) {
-				AlignTask.transformPatchesAndVectorData(la, a);
-			}
+			final LayerSet layerSet = l.getParent();
+			if ( last > first && last < layerSet.size() - 2 )
+				for ( final Layer la : layerSet.getLayers( last + 1, layerSet.size() - 1 ) )
+					AlignTask.transformPatchesAndVectorData( la, a );
+			else if ( first > last && last > 0 )
+				for ( final Layer la : layerSet.getLayers( 0, last - 1 ) )
+					AlignTask.transformPatchesAndVectorData( la, a );
 		}
 	}
 	
-- 
2.11.4.GIT