Add automation for alternating solve

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

@@ -104,6 +104,10 @@ public static void main(final String[] args)
         	cmdLineSetup.parse(args);
         }
 
+		run(cmdLineSetup);
+	}
+
+	public static void run(AffineBlockSolverSetup cmdLineSetup) throws IOException, InterruptedException {
 		final RenderSetup renderSetup = RenderSetup.setupSolve(cmdLineSetup);
 
 		// Note: different setups can be used if specific things need to be done for the solve or certain blocks

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

@@ -0,0 +1,86 @@
+package org.janelia.render.client.newsolver.solvers;
+
+import org.janelia.render.client.ClientRunner;
+import org.janelia.render.client.newsolver.DistributedAffineBlockSolver;
+import org.janelia.render.client.newsolver.setup.AffineBlockSolverSetup;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+
+/**
+ * A solver that alternates between solving for a given block layout and a shifted one so that
+ * all tiles are placed in the center of a block in one of the iterations.
+ * See also: additive Schwarz domain decomposition.
+ *
+ * Author: Michael Innerberger
+ */
+public class AlternatingDomainDecompositionSolverClient {
+
+	private static final int N_RUNS = 4;
+
+	public static void main(String[] args) {
+		if (args.length == 0) {
+			args = new String[]{"--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
+					"--owner", "hess_wafer_53",
+					"--project", "cut_000_to_009",
+					"--matchCollection", "c009_s310_v01_match",
+					"--stack", "c009_s310_v01_mfov_08",
+					"--targetStack", "c009_s310_v01_mfov_08_test",
+					"--minX", "33400",
+					"--maxX", "54600",
+					"--minY", "400",
+					"--maxY", "18700",
+					"--minZ", "424",
+					"--maxZ", "460",
+
+					"--blockSizeX", "7000",
+					"--blockSizeY", "6000",
+					"--shiftBlocks",
+
+					"--completeTargetStack",
+
+					"--maxNumMatches", "0", // no limit, default
+					"--threadsWorker", "1",
+					"--threadsGlobal", "5",
+
+					"--blockOptimizerLambdasRigid", "1.0,1.0,0.9,0.3,0.01",
+					"--blockOptimizerLambdasTranslation", "1.0,0.0,0.0,0.0,0.0",
+					"--blockOptimizerLambdasRegularization", "0.0,0.0,0.0,0.0,0.0",
+					"--blockOptimizerIterations", "50,50,30,25,25",
+					"--blockMaxPlateauWidth", "25,25,15,10,10"
+			};
+		}
+
+		final ClientRunner clientRunner = new ClientRunner(args) {
+			@Override
+			public void runClient(final String[] args) throws Exception {
+
+				final AffineBlockSolverSetup parameters = new AffineBlockSolverSetup();
+				parameters.parse(args);
+
+				LOG.info("runClient: entry, parameters={}", parameters);
+
+				final AlternatingDomainDecompositionSolverClient client =
+						new AlternatingDomainDecompositionSolverClient();
+
+				client.solveAlternating(parameters);
+			}
+		};
+		clientRunner.run();
+	}
+
+	private void solveAlternating(final AffineBlockSolverSetup parameters) throws IOException, InterruptedException {
+		final String targetStackPrefix = parameters.targetStack.stack;
+
+		for (int i = 0; i < N_RUNS; i++) {
+			parameters.targetStack.stack = targetStackPrefix + "_run" + (i + 1);
+			DistributedAffineBlockSolver.run(parameters);
+
+			parameters.blockPartition.shiftBlocks = !parameters.blockPartition.shiftBlocks;
+			parameters.stack = parameters.targetStack.stack;
+		}
+	}
+
+	private static final Logger LOG = LoggerFactory.getLogger(AlternatingDomainDecompositionSolverClient.class);
+}

render-ws-java-client/src/main/java/org/janelia/render/client/parameter/CommandLineParameters.java

@@ -38,7 +38,7 @@ public void parse(final String[] args) throws IllegalArgumentException {
     }
 
     public void parse(final String[] args,
-                      final Class programClass,
+                      final Class<?> programClass,
                       final boolean exitOnHelpOrFailure) throws IllegalArgumentException {
 
         jCommander = new JCommander(this);