Update LeicaHandler plane handling for backwards compatibility

ome · Nov 19, 2024 · 10b48d2 · 10b48d2
1 parent 676dfe6
commit 10b48d2
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Showing 2 changed files with 38 additions and 5 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/LeicaHandler.java b/components/formats-gpl/src/loci/formats/in/LeicaHandler.java
@@ -120,6 +120,7 @@ public class LeicaHandler extends BaseHandler {
   private MetadataLevel level;
   private int laserCount = 0;
 
+  private boolean setPlaneMetadataInStore = true;
   private Map<String, Time> exposureTimes = new HashMap<String, Time>();
   private Map<String, Time> deltaT = new HashMap<String, Time>();
 
@@ -139,6 +140,11 @@ public LeicaHandler(MetadataStore store, MetadataLevel level) {
     this.level = level;
   }
 
+  public LeicaHandler(MetadataStore store, MetadataLevel level, boolean planesInStore) {
+    this(store, level);
+    setPlaneMetadataInStore = planesInStore;
+  }
+
   // -- LeicaHandler API methods --
 
   public List<CoreMetadata> getCoreMetadataList() { return core; }
@@ -556,7 +562,13 @@ else if (id.indexOf("WFC") == 1) {
           try {
             Double exposureTime = DataTools.parseDouble(value);
             if (exposureTime != null) {
-              exposureTimes.put(numDatasets + "-" + c, new Time(exposureTime, UNITS.SECOND));
+              Time expTime = new Time(exposureTime, UNITS.SECOND);
+              if (setPlaneMetadataInStore) {
+                store.setPlaneExposureTime(expTime, numDatasets, c);
+              }
+              else {
+                exposureTimes.put(numDatasets + "-" + c, expTime);
+              }
             }
           }
           catch (IndexOutOfBoundsException e) { }
@@ -885,14 +897,28 @@ else if (qName.equals("TimeStamp") && numDatasets >= 0) {
           store.setImageAcquisitionDate(new Timestamp(date), numDatasets);
         }
         firstStamp = ms;
-        deltaT.put(numDatasets + "-" + count, new Time(0.0, UNITS.SECOND));
+
+        Time stamp = new Time(0.0, UNITS.SECOND);
+        if (setPlaneMetadataInStore) {
+          store.setPlaneDeltaT(stamp, numDatasets, count);
+        }
+        else {
+          deltaT.put(numDatasets + "-" + count, stamp);
+        }
       }
       else if (level != MetadataLevel.MINIMUM) {
         CoreMetadata coreMeta = core.get(numDatasets);
         int nImages = coreMeta.sizeZ * coreMeta.sizeT * coreMeta.sizeC;
         if (count < nImages) {
           ms -= firstStamp;
-          deltaT.put(numDatasets + "-" + count, new Time(ms / 1000.0, UNITS.SECOND));
+
+          Time stamp = new Time(ms / 1000.00, UNITS.SECOND);
+          if (setPlaneMetadataInStore) {
+            store.setPlaneDeltaT(stamp, numDatasets, count);
+          }
+          else {
+            deltaT.put(numDatasets + "-" + count, stamp);
+          }
         }
       }
 
@@ -904,7 +930,14 @@ else if (qName.equals("RelTimeStamp") && level != MetadataLevel.MINIMUM) {
       if (count < nImages) {
         Double time = DataTools.parseDouble(attributes.getValue("Time"));
         if (time != null) {
-          deltaT.put(numDatasets + "-" + count, new Time(time, UNITS.SECOND));
+          Time stamp = new Time(time, UNITS.SECOND);
+          if (setPlaneMetadataInStore) {
+            store.setPlaneDeltaT(stamp, numDatasets, count);
+          }
+          else {
+            deltaT.put(numDatasets + "-" + count, stamp);
+          }
+
           count++;
         }
       }

diff --git a/components/formats-gpl/src/loci/formats/in/TCSReader.java b/components/formats-gpl/src/loci/formats/in/TCSReader.java
@@ -476,7 +476,7 @@ else if (getSizeT() == 1) {
       xml = XMLTools.sanitizeXML(PREFIX + xml + SUFFIX);
 
       LeicaHandler handler =
-        new LeicaHandler(store, getMetadataOptions().getMetadataLevel());
+        new LeicaHandler(store, getMetadataOptions().getMetadataLevel(), false);
       XMLTools.parseXML(xml, handler);
       exposureTime = handler.getExposureTimes();
       deltaT = handler.getDeltaT();