BlockDataSolveParameters creates Worker given a BlockData object

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

@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.List;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -13,6 +12,7 @@
 import org.janelia.render.client.newsolver.blocksolveparameters.FIBSEMAlignmentParameters;
 import org.janelia.render.client.newsolver.setup.AffineSolverSetup;
 import org.janelia.render.client.newsolver.setup.RenderSetup;
+import org.janelia.render.client.newsolver.solvers.Worker;
 import org.janelia.render.client.newsolver.solvers.affine.AffineAlignBlockWorker;
 
 import mpicbg.models.Affine2D;
@@ -24,6 +24,8 @@ public class AffineDistributedSolver
 {
 	final AffineSolverSetup cmdLineSetup;
 	final RenderSetup renderSetup;
+	BlockCollection< ?, AffineModel2D, ? extends FIBSEMAlignmentParameters< ?, ? >, ZBlockFactory > col;
+	ZBlockFactory blockFactory;
 
 	public AffineDistributedSolver(
 			final AffineSolverSetup cmdLineSetup,
@@ -80,16 +82,18 @@ public static void main( final String[] args ) throws IOException
 		// Note: different setups can be used if specific things need to be done for the solve or certain blocks
 		final AffineDistributedSolver solverSetup = new AffineDistributedSolver( cmdLineSetup, renderSetup );
 
-		final ArrayList< ? extends AffineAlignBlockWorker<?, ?, ZBlockFactory > > workers =
+		// create all block instances
+		final BlockCollection< ?, AffineModel2D, ?, ZBlockFactory > blockCollection =
 				solverSetup.setupSolve( cmdLineSetup.blockModel(), cmdLineSetup.stitchingModel() );
 
 		final ExecutorService taskExecutor = Executors.newFixedThreadPool( cmdLineSetup.threadsGlobal );
 
 		taskExecutor.submit( () ->
-			workers.parallelStream().forEach( worker ->
+			blockCollection.allBlocks().parallelStream().forEach( block ->
 			{
 				try
 				{
+					Worker<?, AffineModel2D, ?, ZBlockFactory> worker = block.solveTypeParameters().createWorker( block, solverSetup.col.maxId() + 1, cmdLineSetup.threadsWorker );
 					worker.run();
 				}
 				catch (IOException | ExecutionException | InterruptedException | NoninvertibleModelException e)
@@ -100,17 +104,22 @@ public static void main( final String[] args ) throws IOException
 			}));
 
 		taskExecutor.shutdown();
-
-		for ( final AffineAlignBlockWorker<?, ?, ZBlockFactory > worker : workers )
+		/*
+		for ( final Worker<?, ?, ZBlockFactory > worker : workers )
 		{
-			List<?> blockData = worker.getBlockDataList();
+			ArrayList< ? extends BlockData< ?, AffineModel2D, ?, ? > > blockData = worker.getBlockDataList();
 		}
 
+		// avoid duplicate id assigned while splitting solveitems in the workers
+		// but do keep ids that are smaller or equal to the maxId of the initial solveset
+		final int maxId = SolveTools.fixIds( this.allItems, solverSetup.col.maxId() );
+
 		System.out.println( workers.get( 0 ).getBlockDataList().size() );
+		*/
 	}
 
 	public < M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2D< S > >
-			ArrayList< AffineAlignBlockWorker<M, S, ZBlockFactory > > setupSolve(
+			BlockCollection< M, AffineModel2D, FIBSEMAlignmentParameters< M, S >, ZBlockFactory > setupSolve(
 			final M blockModel,
 			final S stitchingModel )
 	{
@@ -119,22 +128,17 @@ ArrayList< AffineAlignBlockWorker<M, S, ZBlockFactory > > setupSolve(
 		//
 		final ZBlockFactory blockFactory = setupBlockFactory();
 
-		//
-		// setup FIB-SEM solve parameters
-		//
-		final FIBSEMAlignmentParameters< M, S > solveParams =
-				setupSolveParameters( blockModel, stitchingModel );
+		this.blockFactory = blockFactory;
 
 		//
 		// create all blocks
 		//
 		final BlockCollection< M, AffineModel2D, FIBSEMAlignmentParameters< M, S >, ZBlockFactory > col =
-				setupBlockCollection( blockFactory, solveParams );
+				setupBlockCollection( blockFactory, blockModel, stitchingModel );
 
-		//
-		// create workers
-		//
-		return createWorkers( col );
+		this.col = col;
+
+		return col;
 	}
 
 	protected ZBlockFactory setupBlockFactory()
@@ -181,10 +185,17 @@ protected < M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2
 
 	protected < M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2D< S > > BlockCollection< M, AffineModel2D, FIBSEMAlignmentParameters< M, S >, ZBlockFactory > setupBlockCollection(
 			final ZBlockFactory blockFactory,
-			final FIBSEMAlignmentParameters< M, S > solveParams )
+			final M blockModel,
+			final S stitchingModel )
 	{
+		//
+		// setup FIB-SEM solve parameter object
+		//
+		final FIBSEMAlignmentParameters< M, S > defaultSolveParams =
+				setupSolveParameters( blockModel, stitchingModel );
+
 		final BlockCollection< M, AffineModel2D, FIBSEMAlignmentParameters< M, S >, ZBlockFactory > col =
-				blockFactory.defineBlockCollection( rtsc -> solveParams );
+				blockFactory.defineBlockCollection( rtsc -> defaultSolveParams );
 
 		return col;
 	}

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

@@ -1,19 +1,19 @@
 package org.janelia.render.client.newsolver;
 
-import java.util.List;
+import java.util.ArrayList;
 
 import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
 import org.janelia.render.client.newsolver.blocksolveparameters.BlockDataSolveParameters;
 
 import mpicbg.models.CoordinateTransform;
 import mpicbg.models.Model;
 
-public class BlockCollection< M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, P >, F extends BlockFactory< F > > 
+public class BlockCollection< M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, R, P >, F extends BlockFactory< F > > 
 {
-	final List< BlockData< M, R, P, F > > blockDataList;
+	final ArrayList< BlockData< M, R, P, F > > blockDataList;
 	final int minId, maxId;
 
-	public BlockCollection( final List< BlockData< M, R, P, F > > blockDataList )
+	public BlockCollection( final ArrayList< BlockData< M, R, P, F > > blockDataList )
 	{
 		int min = Integer.MAX_VALUE;
 		int max = Integer.MIN_VALUE;
@@ -31,5 +31,5 @@ public BlockCollection( final List< BlockData< M, R, P, F > > blockDataList )
 
 	public int minId() { return minId; }
 	public int maxId() { return maxId; }
-	public List< BlockData< M, R, P, F > > allBlocks() { return blockDataList; }
-}
+	public ArrayList< BlockData< M, R, P, F > > allBlocks() { return blockDataList; }
+}

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

@@ -30,7 +30,7 @@
  * @param <P> - the solve parameters
  * @param <F> - the block factory
  */
-public class BlockData< M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, P >, F extends BlockFactory< F > > implements Serializable
+public class BlockData< M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, R, P >, F extends BlockFactory< F > > implements Serializable
 {
 	private static final long serialVersionUID = -6491517262420660476L;
 
@@ -102,6 +102,8 @@ public ArrayList< Function< Double, Double > > createWeightFunctions()
 
 	public HashMap< Integer, HashSet< String > > zToTileId() { return zToTileId; }
 
+	public void assignUpdatedId( final int id ) { this.id = id; }
+
 	/**
 	 * Fetches basic data for all TileSpecs
 	 *

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

@@ -15,8 +15,8 @@ public abstract class BlockFactory< F extends BlockFactory< F > > implements Ser
 {
 	private static final long serialVersionUID = 5919345114414922447L;
 
-	public abstract <M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, P > > BlockCollection< M, R, P, F > defineBlockCollection(
-			final ParameterProvider< M, P > blockSolveParameterProvider );
+	public abstract <M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, R, P > > BlockCollection< M, R, P, F > defineBlockCollection(
+			final ParameterProvider< M, R, P > blockSolveParameterProvider );
 
 	public abstract ArrayList< Function< Double, Double > > createWeightFunctions( final BlockData< ?, ?, ?, F > block );
 }

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

@@ -3,10 +3,11 @@
 import org.janelia.alignment.spec.ResolvedTileSpecCollection;
 import org.janelia.render.client.newsolver.blocksolveparameters.BlockDataSolveParameters;
 
+import mpicbg.models.CoordinateTransform;
 import mpicbg.models.Model;
 
-public interface ParameterProvider < M extends Model< M >, P extends BlockDataSolveParameters< M, P > >
+public interface ParameterProvider < M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, R, P > >
 {
 	public P create( ResolvedTileSpecCollection rtsc );
-	default public BlockDataSolveParameters< ?,? > basicParameters() { return create( null ); }
+	default public BlockDataSolveParameters< ?,?,? > basicParameters() { return create( null ); }
 }

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

@@ -38,14 +38,13 @@ public ZBlockFactory( final int minZ, final int maxZ, final int blockSize, final
 		this.minBlockSize = minBlockSize;
 	}
 
-	@SuppressWarnings("unchecked")
 	@Override
-	public <M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters<M,P>> BlockCollection<M, R, P, ZBlockFactory> defineBlockCollection(
-			final ParameterProvider< M, P > blockSolveParameterProvider )
+	public <M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters<M,R,P>> BlockCollection<M, R, P, ZBlockFactory> defineBlockCollection(
+			final ParameterProvider< M, R, P > blockSolveParameterProvider )
 	{
 		final List< ZBlockInit > initBlocks = defineBlockLayout( minZ, maxZ, blockSize, minBlockSize );
 
-		final BlockDataSolveParameters< ?,? > basicParameters = blockSolveParameterProvider.basicParameters();
+		final BlockDataSolveParameters< ?,?,? > basicParameters = blockSolveParameterProvider.basicParameters();
 
 		//
 		// fetch metadata from render
@@ -56,7 +55,7 @@ public <M extends Model< M >, R extends CoordinateTransform, P extends BlockData
 				basicParameters.project() );
 
 
-		final List< BlockData< M, R, P, ZBlockFactory > > blockDataList = new ArrayList<>();
+		final ArrayList< BlockData< M, R, P, ZBlockFactory > > blockDataList = new ArrayList<>();
 
 		// for each block, we know the z-range
 		for ( final ZBlockInit initBlock : initBlocks )
@@ -175,6 +174,7 @@ public static List< ZBlockInit > defineBlockLayout( final int minZ, final int ma
 		return Stream.concat( leftSets.stream(), rightSets.stream() ).collect( Collectors.toList() );
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public ArrayList<Function<Double, Double>> createWeightFunctions( final BlockData<?, ?, ?, ZBlockFactory > block)
 	{

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

@@ -2,6 +2,11 @@
 
 import java.io.Serializable;
 
+import org.janelia.render.client.newsolver.BlockData;
+import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
+import org.janelia.render.client.newsolver.solvers.Worker;
+
+import mpicbg.models.CoordinateTransform;
 import mpicbg.models.Model;
 
 /**
@@ -10,7 +15,7 @@
  *
  * @param <M> - the result model type
  */
-public abstract class BlockDataSolveParameters< M extends Model< M >, B extends BlockDataSolveParameters< M, B > > implements Serializable
+public abstract class BlockDataSolveParameters< M extends Model< M >, R extends CoordinateTransform, B extends BlockDataSolveParameters< M, R, B > > implements Serializable
 {
 	private static final long serialVersionUID = -813404780882760053L;
 
@@ -41,4 +46,9 @@ public BlockDataSolveParameters(
 	public String stack() { return stack; }
 
 	public M blockSolveModel() { return blockSolveModel; }
+
+	public abstract < F extends BlockFactory< F > > Worker< M, R, B, F > createWorker(
+			final BlockData< M, R, B, F > blockData,
+			final int startId,
+			final int threadsWorker );
 }

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

@@ -3,7 +3,13 @@
 import java.util.List;
 import java.util.function.Function;
 
+import org.janelia.render.client.newsolver.BlockData;
+import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
+import org.janelia.render.client.newsolver.solvers.Worker;
+import org.janelia.render.client.newsolver.solvers.affine.AffineAlignBlockWorker;
+
 import mpicbg.models.Affine2D;
+import mpicbg.models.AffineModel2D;
 import mpicbg.models.Model;
 
 /**
@@ -13,7 +19,7 @@
  * @param <B> the final block solve type (the result)
  * @param <S> the stitching-first type
  */
-public class FIBSEMAlignmentParameters< M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2D< S > > extends BlockDataSolveParameters< M, FIBSEMAlignmentParameters< M, S> >
+public class FIBSEMAlignmentParameters< M extends Model< M > & Affine2D< M >, S extends Model< S > & Affine2D< S > > extends BlockDataSolveParameters< M, AffineModel2D, FIBSEMAlignmentParameters< M, S > >
 {
 	private static final long serialVersionUID = 4247180309556813829L;
 	public enum PreAlign { NONE, TRANSLATION, RIGID }
@@ -130,4 +136,12 @@ public FIBSEMAlignmentParameters(
 	public int maxIterationsStitching() { return maxIterationsStitching; }
 	public int maxPlateauWidthStitching() { return maxPlateauWidthStitching; }
 
+	@Override
+	public < F extends BlockFactory< F > > Worker< M, AffineModel2D, FIBSEMAlignmentParameters<M, S >, F > createWorker(
+			final BlockData< M, AffineModel2D, FIBSEMAlignmentParameters< M, S >, F > blockData,
+			final int startId,
+			final int threadsWorker )
+	{
+		return new AffineAlignBlockWorker<>( blockData, startId, threadsWorker );
+	}
 }

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

@@ -2,8 +2,15 @@
 
 import mpicbg.models.Affine1D;
 import mpicbg.models.Model;
+
+import org.janelia.render.client.newsolver.BlockData;
+import org.janelia.render.client.newsolver.blockfactories.BlockFactory;
+import org.janelia.render.client.newsolver.solvers.Worker;
+import org.janelia.render.client.newsolver.solvers.affine.AffineAlignBlockWorker;
+import org.janelia.render.client.newsolver.solvers.intensity.AffineIntensityCorrectionBlockWorker;
 import org.janelia.render.client.parameter.IntensityAdjustParameters;
 
+import java.io.IOException;
 import java.util.List;
 
 /**
@@ -13,7 +20,7 @@
  * @param <M> the final block solve type (the result)
  */
 public class FIBSEMIntensityCorrectionParameters<M extends Model<M> & Affine1D<M>>
-		extends BlockDataSolveParameters<M, FIBSEMIntensityCorrectionParameters<M>> {
+		extends BlockDataSolveParameters<M, M, FIBSEMIntensityCorrectionParameters<M>> {
 	private static final long serialVersionUID = -5349107301431384524L;
 
 	final private List<Double> blockOptimizerLambdasTranslation;
@@ -55,4 +62,20 @@ public FIBSEMIntensityCorrectionParameters(
 	public double renderScale() { return intensityParameters.renderScale; }
 	public int numCoefficients() { return intensityParameters.numCoefficients; }
 	public Integer zDistance() { return intensityParameters.zDistance; }
+
+	@Override
+	public <F extends BlockFactory<F>> Worker<M, M, FIBSEMIntensityCorrectionParameters<M>, F> createWorker(
+			final BlockData<M, M, FIBSEMIntensityCorrectionParameters<M>, F> blockData,
+			final int startId,
+			final int threadsWorker )
+	{
+		try
+		{
+			return new AffineIntensityCorrectionBlockWorker<>( blockData, startId, threadsWorker );
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return null;
+		}
+	}
 }

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

@@ -22,7 +22,7 @@
  * @param <P> - the solve parameters
  * @param <F> - the block factory
  */
-public abstract class Worker < M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, P >, F extends BlockFactory< F > > 
+public abstract class Worker < M extends Model< M >, R extends CoordinateTransform, P extends BlockDataSolveParameters< M, R, P >, F extends BlockFactory< F > > 
 {
 	// for assigning new id's when splitting BlockData
 	final protected int startId;