Merge pull request #144 from melissalinkert/unit-unit-test

Expand axes tests to check for correct units
glencoesoftware · May 6, 2022 · b5f6c76 · b5f6c76
2 parents ca1ddc1 + 72b9149
commit b5f6c76
Show file tree

Hide file tree

Showing 2 changed files with 33 additions and 7 deletions.
diff --git 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;
@@ -1617,7 +1621,20 @@ 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
@@ -270,7 +270,7 @@ public void testMultiscalesMetadata() throws Exception {
 
     List<Map<String, Object>> axes =
       (List<Map<String, Object>>) multiscale.get("axes");
-    checkAxes(axes, "TCZYX");
+    checkAxes(axes, "TCZYX", null);
 
     for (int r=0; r<datasets.size(); r++) {
       Map<String, Object> dataset = datasets.get(r);
@@ -320,7 +320,7 @@ public void testSetXYCZTDimensionOrder() throws Exception {
     Map<String, Object> multiscale = multiscales.get(0);
     List<Map<String, Object>> axes =
       (List<Map<String, Object>>) multiscale.get("axes");
-    checkAxes(axes, "TZCYX");
+    checkAxes(axes, "TZCYX", null);
   }
 
   /**
@@ -341,15 +341,15 @@ public void testSetOriginalDimensionOrder() throws Exception {
     Map<String, Object> multiscale = multiscales.get(0);
     List<Map<String, Object>> axes =
       (List<Map<String, Object>>) multiscale.get("axes");
-    checkAxes(axes, "TZCYX");
+    checkAxes(axes, "TZCYX", null);
   }
 
   /**
    * Test that physical sizes are saved in axes/transformations metadata.
    */
   @Test
   public void testPhysicalSizes() throws Exception {
-    input = fake("physicalSizeX", "1.0mm",
+    input = fake("physicalSizeX", "1.0Å",
       "physicalSizeY", "0.5mm",
       "physicalSizeZ", "2cm");
     assertTool();
@@ -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");
+    checkAxes(axes, "TCZYX",
+      new String[] {null, null, "centimeter", "millimeter", "angstrom"});
 
     List<Map<String, Object>> datasets =
       (List<Map<String, Object>>) multiscale.get("datasets");
@@ -1631,12 +1632,20 @@ private void checkWell(
     }
   }
 
-  private void checkAxes(List<Map<String, Object>> axes, String order) {
+  private void checkAxes(List<Map<String, Object>> axes, String order,
+    String[] units)
+  {
     assertEquals(axes.size(), order.length());
     for (int i=0; i<axes.size(); i++) {
       String name = axes.get(i).get("name").toString();
       assertEquals(name, order.toLowerCase().substring(i, i + 1));
       assertTrue(axes.get(i).containsKey("type"));
+      if (units != null) {
+        assertEquals(axes.get(i).get("unit"), units[i]);
+      }
+      else {
+        assertTrue(!axes.get(i).containsKey("unit"));
+      }
     }
   }