From 4a0d8e4c754b3d004692b0c89e38d89c7e80599b Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Mon, 4 Apr 2022 11:20:25 -0500
Subject: [PATCH] Update units to use the enum names instead of symbols

---
 .../bioformats2raw/Converter.java             | 19 ++++++++++++++++++-
 .../bioformats2raw/test/ZarrTest.java         |  3 ++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
index f1703b23..29271318 100644
--- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
+++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -55,11 +55,15 @@
 import loci.formats.ome.OMEXMLMetadata;
 import loci.formats.services.OMEXMLService;
 import loci.formats.services.OMEXMLServiceImpl;
+import ome.units.quantity.Length;
 import ome.units.quantity.Quantity;
+import ome.units.quantity.Time;
 import ome.xml.meta.OMEXMLMetadataRoot;
 import ome.xml.model.enums.DimensionOrder;
 import ome.xml.model.enums.EnumerationException;
 import ome.xml.model.enums.PixelType;
+import ome.xml.model.enums.UnitsLength;
+import ome.xml.model.enums.UnitsTime;
 import ome.xml.model.primitives.PositiveInteger;
 
 import org.perf4j.slf4j.Slf4JStopWatch;
@@ -1610,7 +1614,20 @@ else if (axis.equals("c")) {
       thisAxis.put("name", axis);
       thisAxis.put("type", type);
       if (scale != null) {
-        thisAxis.put("unit", scale.unit().getSymbol());
+        String symbol = scale.unit().getSymbol();
+        String unitName = null;
+        try {
+          if (scale instanceof Length) {
+            unitName = UnitsLength.fromString(symbol).name().toLowerCase();
+          }
+          else if (scale instanceof Time) {
+            unitName = UnitsTime.fromString(symbol).name().toLowerCase();
+          }
+        }
+        catch (EnumerationException e) {
+          LOGGER.warn("Could not identify unit '{}'", symbol);
+        }
+        thisAxis.put("unit", unitName);
       }
       axes.add(thisAxis);
     }
diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
index a076c2e7..abdf04c8 100644
--- a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
+++ b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -361,7 +361,8 @@ public void testPhysicalSizes() throws Exception {
     Map<String, Object> multiscale = multiscales.get(0);
     List<Map<String, Object>> axes =
       (List<Map<String, Object>>) multiscale.get("axes");
-    checkAxes(axes, "TCZYX", new String[] {null, null, "cm", "mm", "mm"});
+    checkAxes(axes, "TCZYX",
+      new String[] {null, null, "centimeter", "millimeter", "millimeter"});
 
     List<Map<String, Object>> datasets =
       (List<Map<String, Object>>) multiscale.get("datasets");