implemented generic assembly of blocks for the trivial case

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/AffineDistributedSolver.java

@@ -3,6 +3,8 @@
 import java.io.IOException;
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 import java.util.concurrent.Callable;
 import java.util.concurrent.CompletableFuture;
@@ -12,6 +14,7 @@
 import java.util.concurrent.Future;
 import java.util.function.Function;
 
+import org.janelia.alignment.spec.ResolvedTileSpecCollection.TransformApplicationMethod;
 import org.janelia.render.client.newsolver.blockfactories.ZBlockFactory;
 import org.janelia.render.client.newsolver.blocksolveparameters.FIBSEMAlignmentParameters;
 import org.janelia.render.client.newsolver.setup.AffineSolverSetup;
@@ -21,7 +24,9 @@
 import org.janelia.render.client.newsolver.solvers.affine.AffineAlignBlockWorker;
 import org.janelia.render.client.solver.DistributedSolveDeSerialize;
 import org.janelia.render.client.solver.DistributedSolveWorker;
+import org.janelia.render.client.solver.MinimalTileSpec;
 import org.janelia.render.client.solver.SolveItemData;
+import org.janelia.render.client.solver.SolveTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -152,6 +157,35 @@ public static void main( final String[] args ) throws IOException
 		final int maxId = WorkerTools.fixIds( allItems, solverSetup.col.maxId() );
 
 		LOG.info( "computed " + allItems.size() + " blocks, maxId=" + maxId);
+
+		/*
+		//
+		// Saving the result
+		//
+		LOG.info( "Saving targetstack=" + cmdLineSetup.targetStack );
+
+		//
+		// save the re-aligned part
+		//
+		final HashSet< Double > zToSaveSet = new HashSet<>();
+
+		for ( final TileSpec ts : solve.idToTileSpecGlobal.values() )
+			zToSaveSet.add( ts.getZ() );
+
+		List< Double > zToSave = new ArrayList<>( zToSaveSet );
+		Collections.sort( zToSave );
+
+		LOG.info("Saving from " + zToSave.get( 0 ) + " to " + zToSave.get( zToSave.size() - 1 ) );
+
+		SolveTools.saveTargetStackTiles( parameters.stack, parameters.targetStack, runParams, solve.idToFinalModelGlobal, null, zToSave, TransformApplicationMethod.REPLACE_LAST );
+
+		if ( parameters.completeTargetStack )
+		{
+			LOG.info( "Completing targetstack=" + parameters.targetStack );
+
+			SolveTools.completeStack( parameters.targetStack, runParams );
+		}
+		*/
 	}
 
 	public < M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2D< S > >

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/assembly/Affine2DZBlockAssembler.java

@@ -0,0 +1,26 @@
+package org.janelia.render.client.newsolver.assembly;
+
+import java.util.List;
+
+import org.janelia.render.client.newsolver.BlockData;
+import org.janelia.render.client.newsolver.blockfactories.ZBlockFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import mpicbg.models.AffineModel2D;
+
+public class Affine2DZBlockAssembler extends Assembler< AffineModel2D, ZBlockFactory >
+{
+
+	public Affine2DZBlockAssembler( final List<BlockData<?, AffineModel2D, ?, ZBlockFactory>> blocks, final int startId)
+	{
+		super( blocks, startId );
+	}
+
+	@Override
+	public void assemble(  )
+	{
+	}
+
+	private static final Logger LOG = LoggerFactory.getLogger(Affine2DZBlockAssembler.class);
+}

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/assembly/Assembler.java

@@ -0,0 +1,97 @@
+package org.janelia.render.client.newsolver.assembly;
+
+import java.util.HashSet;
+import java.util.List;
+
+import org.janelia.render.client.newsolver.BlockData;
+import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import mpicbg.models.CoordinateTransform;
+
+public abstract class Assembler< R extends CoordinateTransform, F extends BlockFactory< F > >
+{
+	final List<BlockData<?, R, ?, F> > blocks;
+
+	int id;
+
+	public Assembler( final List<BlockData<?, R, ?, F> > blocks, final int startId )
+	{
+		this.id = startId;
+		this.blocks = blocks;
+	}
+
+	public AssemblyMaps< R > getAssembly()
+	{
+		AssemblyMaps< R > am;
+
+		// the trivial case of a single block, would crash with the code below
+		if ( ( am = handleTrivialCase() ) != null )
+			return am;
+		else
+			am = new AssemblyMaps< R >();
+
+		assemble();
+
+		return null;
+	}
+
+	public abstract void assemble();
+
+	/**
+	 * 
+	 * @return - the result of the trivial case if it was a single block
+	 */
+	protected AssemblyMaps< R > handleTrivialCase()
+	{
+		if ( blocks.size() == 1 )
+		{
+			LOG.info( "Assembler: only a single block, no solve across blocks necessary." );
+
+			final AssemblyMaps< R > am = new AssemblyMaps< R >();
+
+			final BlockData< ?, R, ?, F > solveItem = blocks.get( 0 );
+
+			for ( int z = solveItem.minZ(); z <= solveItem.maxZ(); ++z )
+			{
+				// there is no overlap with any other solveItem (should be beginning or end of the entire stack)
+				final HashSet< String > tileIds = solveItem.zToTileId().get( z );
+
+				// if there are none, we continue with the next
+				if ( tileIds.size() == 0 )
+					continue;
+
+				am.zToTileIdGlobal.putIfAbsent( z, new HashSet<>() );
+
+				for ( final String tileId : tileIds )
+				{
+					am.zToTileIdGlobal.get( z ).add( tileId );
+					am.idToTileSpecGlobal.put( tileId, solveItem.rtsc().getTileSpec( tileId ) );
+					am.idToFinalModelGlobal.put( tileId, solveItem.idToNewModel().get( tileId ) );
+				}
+			}
+
+			return am;
+		}
+		else
+		{
+			return null;
+		}
+	}
+
+	/*
+	public static ResolvedTileSpecCollection combineAllTileSpecs( final List< BlockData<?, ?, ?, ?> > allItems )
+	{
+		final ResolvedTileSpecCollection rtsc = new ResolvedTileSpecCollection();
+
+		// TODO trautmane - improve this
+		// this should automatically get rid of duplicates due to the common tileId
+		for ( BlockData<?, ?, ?, ?> block : allItems )
+			block.rtsc().getTileSpecs().forEach( tileSpec -> rtsc.addTileSpecToCollection( tileSpec ) );
+
+		return rtsc;
+	}*/
+
+	private static final Logger LOG = LoggerFactory.getLogger(Assembler.class);
+}

render-ws-java-client/src/main/java/org/janelia/render/client/newsolver/assembly/AssemblyMaps.java

@@ -0,0 +1,18 @@
+package org.janelia.render.client.newsolver.assembly;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+
+import org.janelia.alignment.spec.TileSpec;
+
+import mpicbg.models.CoordinateTransform;
+import net.imglib2.util.Pair;
+
+public class AssemblyMaps< R extends CoordinateTransform >
+{
+	final public HashMap< String, R > idToFinalModelGlobal = new HashMap<>();
+	final public HashMap< String, TileSpec > idToTileSpecGlobal = new HashMap<>();
+	final public HashMap<Integer, HashSet<String> > zToTileIdGlobal = new HashMap<>();
+	final public HashMap< String, List< Pair< String, Double > > > idToErrorMapGlobal = new HashMap<>();
+}