SVS: populate plane position for full-resolution image

Fixes ome#3743
melissalinkert · Aug 11, 2023 · 593c819 · 593c819
1 parent 1b6da10
commit 593c819
Showing 1 changed file with 28 additions and 1 deletion.
diff --git a/components/formats-gpl/src/loci/formats/in/SVSReader.java b/components/formats-gpl/src/loci/formats/in/SVSReader.java
@@ -100,6 +100,9 @@ public class SVSReader extends BaseTiffReader {
   // total number of extra (label and macro) images
   private int extraImages = 0;
 
+  private transient Double physicalDistanceFromLeftEdge;
+  private transient Double physicalDistanceFromTopEdge;
+
   // -- Constructor --
 
   /** Constructs a new SVS reader. */
@@ -481,6 +484,12 @@ else if (t.toLowerCase().indexOf("macro") >= 0) {
                   int color = Integer.parseInt(value);
                   displayColor = new Color((color << 8) | 0xff);
                   break;
+                case "Left":
+                  physicalDistanceFromLeftEdge = DataTools.parseDouble(value);
+                  break;
+                case "Top":
+                  physicalDistanceFromTopEdge = DataTools.parseDouble(value);
+                  break;
               }
             }
           }
@@ -498,7 +507,10 @@ protected void initMetadataStore() throws FormatException {
     super.initMetadataStore();
 
     MetadataStore store = makeFilterMetadata();
-    MetadataTools.populatePixels(store, this, getImageCount() > 1);
+    boolean populatePlaneData = getImageCount() > 1 ||
+      physicalDistanceFromTopEdge != null ||
+      physicalDistanceFromLeftEdge != null;
+    MetadataTools.populatePixels(store, this, populatePlaneData);
 
     String instrument = MetadataTools.createLSID("Instrument", 0);
     String objective = MetadataTools.createLSID("Objective", 0, 0);
@@ -513,6 +525,21 @@ protected void initMetadataStore() throws FormatException {
       store.setImageInstrumentRef(instrument, i);
       store.setObjectiveSettingsID(objective, i);
 
+      if (i == 0) {
+        if (physicalDistanceFromTopEdge != null) {
+          Length yPos = FormatTools.getStagePosition(physicalDistanceFromTopEdge, UNITS.MM);
+          for (int p=0; p<getImageCount(); p++) {
+            store.setPlanePositionY(yPos, i, p);
+          }
+        }
+        if (physicalDistanceFromLeftEdge != null) {
+          Length xPos = FormatTools.getStagePosition(physicalDistanceFromLeftEdge, UNITS.MM);
+          for (int p=0; p<getImageCount(); p++) {
+            store.setPlanePositionX(xPos, i, p);
+          }
+        }
+      }
+
       if (hasFlattenedResolutions() || i > extraImages) {
         store.setImageName("Series " + (i + 1), i);
       }