From 5ecedc91879912721b66bed1d314f6b2a7ac3939 Mon Sep 17 00:00:00 2001
From: Michael Innerberger <innerbergerm@hhmi.org>
Date: Tue, 26 Mar 2024 18:44:22 -0400
Subject: [PATCH] Reorder tiles by changing their tileIds

---
 .../render/client/TileReorderingClient.java   | 34 ++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

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
index 2ae1ae93f..c9c002087 100644
--- 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
@@ -3,13 +3,17 @@
 import com.beust.jcommander.Parameter;
 import com.beust.jcommander.ParametersDelegate;
 import org.janelia.alignment.spec.ResolvedTileSpecCollection;
+import org.janelia.alignment.spec.TileSpec;
 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.Arrays;
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * This client reorders the tiles in a multi-sem stack in a way that the rendering order
@@ -43,7 +47,7 @@ public static void main(final String[] args) {
 				"--owner", "hess_wafer_53b",
 				"--project", "cut_070_to_079",
 				"--stack", "c070_s032_v01_align_ic",
-				"--targetStack", "c070_s032_v01_mi_reordering_test"
+				"--targetStack", "c070_s032_v01_mi_reordering_test_scan_order"
 		};
 		final ClientRunner clientRunner = new ClientRunner(xargs) {
 			@Override
@@ -67,6 +71,22 @@ public void runClient(final String[] args) throws Exception {
 	private final Parameters parameters;
 	private final RenderDataClient dataClient;
 
+	// The new order of the tiles in the multi-sem stack:
+	// Number the tiles in an SFOV from 1 to 91, starting in the top left corner and going
+	// row by row. Then, record these numbers in the original order of the tiles (i.e.,
+	// starting in the middle of the SFOV and spiraling outwards counterclockwise).
+	private final int[] newNumber = {
+			46, 47, 36, 35, 45, 56, 57, 48, 37, 27,
+			26, 25, 34, 44, 55, 65, 66, 67, 58, 49,
+			38, 28, 19, 18, 17, 16, 24, 33, 43, 54,
+			64, 73, 74, 75, 76, 68, 59, 50, 39, 29,
+			20, 12, 11, 10,  9,  8, 15, 23, 32, 42,
+			53, 63, 72, 80, 81, 82, 83, 84, 77, 69,
+			60, 51, 40, 30, 21, 13,  6,  5,  4,  3,
+			 2,  1,  7, 14, 22, 31, 41, 52, 62, 71,
+			79, 86, 87, 88, 89, 90, 91, 85, 78, 70, 61
+	};
+
 	private TileReorderingClient(final Parameters parameters) {
 		this.parameters = parameters;
 		this.dataClient = parameters.renderWeb.getDataClient();
@@ -94,10 +114,22 @@ 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());
 
+		for (final String tileId : sourceCollection.getTileIds()) {
+			final TileSpec tileSpec = sourceCollection.getTileSpec(tileId);
+			tileSpec.setTileId(updateSfovNumber(tileId));
+		}
+
 		if (sourceCollection.getTileCount() > 0) {
 			dataClient.saveResolvedTiles(sourceCollection, parameters.targetStack, z);
 		}
 	}
 
+	private String updateSfovNumber(final String tileId) {
+		final String[] tileIdComponents = tileId.split("_");
+		final int oldNumber = Integer.parseInt(tileIdComponents[2]);
+		tileIdComponents[2] = String.format("%03d", newNumber[oldNumber - 1]);
+		return String.join("_", tileIdComponents);
+	}
+
 	private static final Logger LOG = LoggerFactory.getLogger(TileReorderingClient.class);
 }