From 6f612a57022f003691421314298d34bbc2afea7c Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 2 Oct 2024 12:46:40 -0500
Subject: [PATCH] Add `--no-tiles` option to write metadata only

---
 .../bioformats2raw/Converter.java             | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index ca54f63..d2f770e 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -167,6 +167,7 @@ public class Converter implements Callable<Integer> {
   private volatile boolean noRootGroup = false;
   private volatile boolean reuseExistingResolutions = false;
   private volatile int minSize;
+  private volatile boolean writeImageData = true;
 
   /** Scaling implementation that will be used during downsampling. */
   private volatile IImageScaler scaler = new SimpleImageScaler();
@@ -374,6 +375,20 @@ public void setChunkDepth(int depth) {
     }
   }
 
+  /**
+   * Set whether or not tiles should actually be converted.
+   *
+   * @param noTiles true if tiles should not be converted
+   */
+  @Option(
+    names = {"--no-tiles"},
+    description = "Write all metadata, but do not convert any tiles",
+    defaultValue = "false"
+  )
+  public void setNoTiles(boolean noTiles) {
+    writeImageData = !noTiles;
+  }
+
   /**
    * Set the slf4j logging level. Defaults to "WARN".
    *
@@ -930,6 +945,13 @@ public int getChunkDepth() {
     return chunkDepth;
   }
 
+  /**
+   * @return true if image data will not be converted
+   */
+  public boolean getNoTiles() {
+    return !writeImageData;
+  }
+
   /**
    * @return slf4j logging level
    */
@@ -2132,6 +2154,10 @@ public void saveResolutions(int series)
               compressionType.toString(), compressionProperties));
       ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);
 
+      if (!writeImageData) {
+        continue;
+      }
+
       nTile = new AtomicInteger(0);
       tileCount = resTileCounts[resolution];