From 13aa28d657c5340bb1a2ecbb40c5847e911c3162 Mon Sep 17 00:00:00 2001
From: Michael Innerberger <innerbergerm@hhmi.org>
Date: Tue, 26 Mar 2024 15:36:09 -0400
Subject: [PATCH] Set up client that copies tiles from one stack to the next

---
 .../render/client/TileReorderingClient.java   | 103 ++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 render-ws-java-client/src/main/java/org/janelia/render/client/TileReorderingClient.java

diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/TileReorderingClient.java b/render-ws-java-client/src/main/java/org/janelia/render/client/TileReorderingClient.java
new file mode 100644
index 000000000..2ae1ae93f
--- /dev/null
+++ b/render-ws-java-client/src/main/java/org/janelia/render/client/TileReorderingClient.java
@@ -0,0 +1,103 @@
+package org.janelia.render.client;
+
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParametersDelegate;
+import org.janelia.alignment.spec.ResolvedTileSpecCollection;
+import org.janelia.alignment.spec.stack.StackMetaData;
+import org.janelia.render.client.parameter.CommandLineParameters;
+import org.janelia.render.client.parameter.RenderWebServiceParameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.util.List;
+
+/**
+ * This client reorders the tiles in a multi-sem stack in a way that the rendering order
+ * causes overlapping tiles to be rendered in the correct order. (I.e., the tile where
+ * the overlapping region is imaged first is on top.)
+ *
+ * @author Michael Innerberger
+ */
+public class TileReorderingClient {
+	public static class Parameters extends CommandLineParameters {
+
+		@ParametersDelegate
+		public RenderWebServiceParameters renderWeb = new RenderWebServiceParameters();
+
+		@Parameter(
+				names = "--stack",
+				description = "Name of source stack",
+				required = true)
+		public String stack;
+
+		@Parameter(
+				names = "--targetStack",
+				description = "Name of target stack",
+				required = true)
+		public String targetStack;
+	}
+
+	public static void main(final String[] args) {
+		final String[] xargs = {
+				"--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
+				"--owner", "hess_wafer_53b",
+				"--project", "cut_070_to_079",
+				"--stack", "c070_s032_v01_align_ic",
+				"--targetStack", "c070_s032_v01_mi_reordering_test"
+		};
+		final ClientRunner clientRunner = new ClientRunner(xargs) {
+			@Override
+			public void runClient(final String[] args) throws Exception {
+
+				final Parameters parameters = new Parameters();
+				parameters.parse(args);
+
+				LOG.info("runClient: entry, parameters={}", parameters);
+
+				final TileReorderingClient client = new TileReorderingClient(parameters);
+
+				client.setUpTargetStack();
+				client.transferTileSpecs();
+				client.completeTargetStack();
+			}
+		};
+		clientRunner.run();
+	}
+
+	private final Parameters parameters;
+	private final RenderDataClient dataClient;
+
+	private TileReorderingClient(final Parameters parameters) {
+		this.parameters = parameters;
+		this.dataClient = parameters.renderWeb.getDataClient();
+	}
+
+	private void setUpTargetStack() throws Exception {
+		final StackMetaData sourceStackMetaData = dataClient.getStackMetaData(parameters.stack);
+		dataClient.setupDerivedStack(sourceStackMetaData, parameters.targetStack);
+		LOG.info("setUpTargetStack: setup stack {}", parameters.targetStack);
+	}
+
+	private void completeTargetStack() throws Exception {
+		dataClient.setStackState(parameters.targetStack, StackMetaData.StackState.COMPLETE);
+		LOG.info("completeTargetStack: setup stack {}", parameters.targetStack);
+	}
+
+	private void transferTileSpecs() throws Exception {
+		final List<Double> zValues = dataClient.getStackZValues(parameters.stack);
+		for (final Double z : zValues) {
+			transferLayer(z);
+		}
+	}
+
+	private void transferLayer(final Double z) throws Exception {
+		final ResolvedTileSpecCollection sourceCollection = dataClient.getResolvedTiles(parameters.stack, z);
+		LOG.info("transferLayer: transferring layer {} with {} tiles", z, sourceCollection.getTileCount());
+
+		if (sourceCollection.getTileCount() > 0) {
+			dataClient.saveResolvedTiles(sourceCollection, parameters.targetStack, z);
+		}
+	}
+
+	private static final Logger LOG = LoggerFactory.getLogger(TileReorderingClient.class);
+}