From 6c6c0c56ff965a73fe7e46bb41111bca787a569c Mon Sep 17 00:00:00 2001
From: Albert Cardona <acardona@ini.phys.ethz.ch>
Date: Tue, 21 Apr 2009 15:31:22 -0400
Subject: [PATCH] Now importing a sequence as grid and related use the new
 AlignTask

---
 ini/trakem2/imaging/StitchingTEM.java |  7 +++-
 mpicbg/trakem2/align/AlignTask.java   | 77 ++++++++++++++++++++++++++++++-----
 2 files changed, 72 insertions(+), 12 deletions(-)

diff --git a/ini/trakem2/imaging/StitchingTEM.java b/ini/trakem2/imaging/StitchingTEM.java
index 7beab998..ef8a05f1 100644
--- a/ini/trakem2/imaging/StitchingTEM.java
+++ b/ini/trakem2/imaging/StitchingTEM.java
@@ -65,6 +65,7 @@ import java.util.Iterator;
 import java.util.Vector;
 import java.awt.geom.AffineTransform;
 
+import mpicbg.trakem2.align.AlignTask;
 
 /** Given:
  *  - list of images
@@ -144,9 +145,11 @@ public class StitchingTEM {
 			case StitchingTEM.TOP_LEFT_RULE:
 				return StitchingTEM.stitchTopLeft(patch, grid_width, percent_overlap, (scale > 1 ? 1 : scale), default_bottom_top_overlap, default_left_right_overlap, optimize);
 			case StitchingTEM.FREE_RULE:
-				HashSet<Patch> hs = new HashSet<Patch>();
+				final HashSet<Patch> hs = new HashSet<Patch>();
 				for (int i=0; i<patch.length; i++) hs.add(patch[i]);
-				return Registration.registerTilesSIFT(hs, patch[0], null, true);
+				final ArrayList<Patch> fixed = new ArrayList<Patch>();
+				fixed.add(patch[0]);
+				return AlignTask.alignPatchesTask( new ArrayList<Patch>(hs), fixed );
 		}
 		return null;
 	}
diff --git a/mpicbg/trakem2/align/AlignTask.java b/mpicbg/trakem2/align/AlignTask.java
index 0ae46561..949342d6 100644
--- a/mpicbg/trakem2/align/AlignTask.java
+++ b/mpicbg/trakem2/align/AlignTask.java
@@ -68,22 +68,83 @@ final public class AlignTask
 		};
 		return Bureaucrat.createAndStart( worker, selection.getProject() );
 	}
-	
-		
+
+
 	final static public void alignSelection( final Selection selection )
 	{
 		List< Patch > patches = new ArrayList< Patch >();
-		for ( Displayable d : Display.getFront().getSelection().getSelected() )
+		for ( Displayable d : selection.getSelected() )
 			if ( d instanceof Patch ) patches.add( ( Patch )d );
 
+		List< Patch > fixedPatches = new ArrayList< Patch >();
+
+		// Add active Patch, if any, as the nail
+		Displayable active = selection.getActive();
+		if ( null != active && active instanceof Patch )
+			fixedPatches.add( (Patch)active );
+
+		// Add all locked Patch instances to fixedPatches
+		for (final Patch patch : patches)
+			if ( patch.isLocked() )
+				fixedPatches.add( patch );
+
+		alignPatches( patches, fixedPatches );
+	}
+
+	final static public Bureaucrat alignPatchesTask ( final List< Patch > patches , final List< Patch > fixedPatches )
+	{
+		if ( 0 == patches.size())
+		{
+			Utils.log("Can't align zero patches.");
+			return null;
+		}
+		Worker worker = new Worker("Aligning images", false, true) {
+			public void run() {
+				startedWorking();
+				try {
+					alignPatches( patches, fixedPatches );
+					Display.repaint();
+				} catch (Throwable e) {
+					IJError.print(e);
+				} finally {
+					finishedWorking();
+				}
+			}
+			public void cleanup() {
+				patches.get(0).getLayer().getParent().undoOneStep();
+			}
+		};
+		return Bureaucrat.createAndStart( worker, patches.get(0).getProject() );
+	}
+
+	/**
+	 * @param patches: the list of Patch instances to align, all belonging to the same Layer.
+	 * @param fixed: the list of Patch instances to keep locked in place, if any.
+	 */
+	final static public void alignPatches( final List< Patch > patches , final List< Patch > fixedPatches )
+	{
 		if ( patches.size() < 2 )
 		{
-			Utils.log("No images to align in the selection.");
+			Utils.log("No images to align.");
 			return;
 		}
-		
+
+		for ( final Patch patch : fixedPatches )
+		{
+			if ( !patches.contains( patch ) )
+			{
+				Utils.log("The list of fixed patches contains at least one Patch not included in the list of patches to align!");
+				return;
+			}
+			if ( patch.isLinked() && !patch.isOnlyLinkedTo( Patch.class ) )
+			{
+				Utils.log("At least one Patch is linked to non-image data, can't align!");
+				return;
+			}
+		}
+
 		//final Align.ParamOptimize p = Align.paramOptimize;
-		final GenericDialog gd = new GenericDialog( "Align Selected Tiles" );
+		final GenericDialog gd = new GenericDialog( "Align Tiles" );
 		Align.paramOptimize.addFields( gd );
 		
 		gd.addMessage( "Miscellaneous:" );
@@ -102,10 +163,6 @@ final public class AlignTask
 		deleteDisconnectedTiles = gd.getNextBoolean();
 		
 		final Align.ParamOptimize p = Align.paramOptimize.clone();
-		List< Patch > fixedPatches = new ArrayList< Patch >();
-		final Displayable active = selection.getActive();
-		if ( active != null && active instanceof Patch )
-			fixedPatches.add( ( Patch )active );
 
 		List< AbstractAffineTile2D< ? > > tiles = new ArrayList< AbstractAffineTile2D< ? > >();
 		List< AbstractAffineTile2D< ? > > fixedTiles = new ArrayList< AbstractAffineTile2D< ? > > ();
-- 
2.11.4.GIT