add main class, keep implementing re-do FIBSEM align

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

@@ -7,7 +7,6 @@
 import org.janelia.render.client.newsolver.blocksolveparameters.BlockDataSolveParameters;
 import org.janelia.render.client.solver.MinimalTileSpec;
 
-import mpicbg.models.AffineModel2D;
 import mpicbg.models.Model;
 
 /**
@@ -23,7 +22,10 @@ public class BlockData< M extends Model< M > > implements Serializable
 
 	private int id;
 
-	// contains solve-specific paramters and models
+	// the BlockFactory that created this BlockData
+	final BlockFactory factory;
+
+	// contains solve-specific parameters and models
 	final BlockDataSolveParameters<M> solveTypeParameters;
 
 	// used for global solve outside
@@ -41,6 +43,7 @@ public BlockData(
 			final int id )
 	{
 		this.id = id;
+		this.factory = factory;
 		this.solveTypeParameters = solveTypeParameters;
 	}
 

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

@@ -0,0 +1,85 @@
+package org.janelia.render.client.newsolver;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.function.Function;
+
+import org.janelia.render.client.newsolver.blockfactories.ZBlock;
+import org.janelia.render.client.newsolver.blocksolveparameters.FIBSEMSolveParameters;
+import org.janelia.render.client.solver.DistributedSolveParameters;
+import org.janelia.render.client.solver.RunParameters;
+
+import mpicbg.models.Affine2D;
+
+public class DistributedSolver
+{
+	public static void main( String[] args ) throws IOException
+	{
+        final DistributedSolveParameters parameters = new DistributedSolveParameters();
+
+        // TODO: remove testing hack ...
+        if (args.length == 0) {
+            final String[] testArgs = {
+                    "--baseDataUrl", "http://tem-services.int.janelia.org:8080/render-ws/v1",
+                    "--owner", "Z0720_07m_BR", //"flyem", //"cosem", //"Z1217_33m_BR",
+                    "--project", "Sec24", //"Z0419_25_Alpha3", //"jrc_hela_2", //"Sec10",
+                    "--matchCollection", "Sec24_v1", //"Sec32_v1", //"Z0419_25_Alpha3_v1", //"jrc_hela_2_v1", //"Sec10_multi",
+
+                    "--stack", "v5_acquire_trimmed",
+                    "--targetStack", "v5_acquire_trimmed_test",
+//                    "--minZ", "1234",
+//                    "--maxZ", "1234",
+
+//                    "--completeTargetStack",
+//                    "--visualizeResults",
+
+                    // note: prealign is with translation only
+                    "--blockOptimizerLambdasRigid",       "1.0,1.0,0.9,0.3,0.01",
+                    "--blockOptimizerLambdasTranslation", "1.0,0.0,0.0,0.0,0.0",
+                    "--blockOptimizerIterations", "100,100,50,25,25",
+                    "--blockMaxPlateauWidth", "25,25,15,10,10",
+                    //"--blockOptimizerIterations", "1000,1000,500,250,250",
+                    //"--blockMaxPlateauWidth", "250,250,150,100,100",
+
+                    //"--blockSize", "100",
+                    "--minStitchingInliers", "100000000",// do not stitch first
+                    "--maxNumMatches", "0", // no limit, default
+                    "--threadsWorker", "1", 
+                    "--threadsGlobal", "60",
+                    "--maxPlateauWidthGlobal", "50",
+                    "--maxIterationsGlobal", "10000",
+            };
+            parameters.parse(testArgs);
+        } else {
+            parameters.parse(args);
+        }
+
+		RunParameters runParameters = DistributedSolveParameters.setupSolve( parameters );
+
+		//
+		// setup Z BlockFactory
+		//
+		final int minZ = (int)Math.round( runParameters.minZ );
+		final int maxZ = (int)Math.round( runParameters.maxZ );
+		final int blockSize = parameters.blockSize;
+		final int minBlockSize = parameters.minBlockSize;
+
+		final BlockFactory blockFactory = new ZBlock( minZ, maxZ, blockSize, minBlockSize );
+
+		//
+		// setup FIB-SEM solve parameters
+		//
+		final boolean rigidPreAlign = false;
+
+		FIBSEMSolveParameters solveParams = new FIBSEMSolveParameters(
+				null, //parameters.blockModel(),
+				(Function< Integer, Affine2D<?> > & Serializable )(z) -> parameters.stitchingModel(),
+				(Function< Integer, Integer > & Serializable )(z) -> parameters.minStitchingInliers,
+				parameters.blockOptimizerLambdasRigid,
+				parameters.blockOptimizerLambdasTranslation,
+				parameters.blockOptimizerIterations,
+				parameters.blockMaxPlateauWidth,
+				parameters.blockMaxAllowedError,
+				rigidPreAlign );
+	}
+}

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

@@ -2,15 +2,15 @@
 
 import java.io.Serializable;
 
-import mpicbg.models.Model;
+import mpicbg.models.CoordinateTransform;
 
 /**
  * 
  * @author preibischs
  *
  * @param <M> - the result model type
  */
-public class BlockDataSolveParameters< M extends Model<M> > implements Serializable
+public class BlockDataSolveParameters< M extends CoordinateTransform > implements Serializable
 {
 	private static final long serialVersionUID = -813404780882760053L;
 

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

@@ -17,9 +17,6 @@ public class FIBSEMSolveParameters< B extends Model< B > & Affine2D< B >, S exte
 {
 	private static final long serialVersionUID = 4247180309556813829L;
 
-	final int minZ;
-	final int maxZ;
-
 	final private B blockSolveModel;
 	final private Function< Integer, S > stitchingModelSupplier;
 	final private Function< Integer, Integer > minStitchingInliersSupplier; // if it is less, it is not stitched first
@@ -41,9 +38,7 @@ public FIBSEMSolveParameters(
 			final List<Integer> blockOptimizerIterations,
 			final List<Integer> blockMaxPlateauWidth,
 			final double blockMaxAllowedError,
-			final boolean rigidPreAlign,
-			final int minZ,
-			final int maxZ )
+			final boolean rigidPreAlign )
 	{
 		this.blockSolveModel = blockSolveModel.copy();
 		this.stitchingModelSupplier = stitchingModelSupplier;
@@ -54,13 +49,8 @@ public FIBSEMSolveParameters(
 		this.blockMaxPlateauWidth = blockMaxPlateauWidth;
 		this.blockMaxAllowedError = blockMaxAllowedError;
 		this.rigidPreAlign = rigidPreAlign;
-		this.minZ = minZ;
-		this.maxZ = maxZ;
 	}
 
-	public int minZ() { return minZ; }
-	public int maxZ() { return maxZ; }
-
 	public B blockSolveModelInstance() { return blockSolveModel.copy(); }
 
 	public S stitchingSolveModelInstance( final int z ) { return stitchingModelSupplier.apply( z ); }