Don't set Plane metadata until we know the final plane counts

melissalinkert · Nov 11, 2024 · 676dfe6 · 676dfe6
1 parent 5a00e83
commit 676dfe6
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Showing 2 changed files with 32 additions and 4 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 +120,9 @@ public class LeicaHandler extends BaseHandler {
   private MetadataLevel level;
   private int laserCount = 0;
 
+  private Map<String, Time> exposureTimes = new HashMap<String, Time>();
+  private Map<String, Time> deltaT = new HashMap<String, Time>();
+
   // -- Constructor --
 
   public LeicaHandler(MetadataStore store, MetadataLevel level) {
@@ -144,6 +147,10 @@ public LeicaHandler(MetadataStore store, MetadataLevel level) {
 
   public Vector<String> getLutNames() { return lutNames; }
 
+  public Map<String, Time> getExposureTimes() { return exposureTimes; }
+
+  public Map<String, Time> getDeltaT() { return deltaT; }
+
   // -- DefaultHandler API methods --
 
   @Override
@@ -549,7 +556,7 @@ else if (id.indexOf("WFC") == 1) {
           try {
             Double exposureTime = DataTools.parseDouble(value);
             if (exposureTime != null) {
-              store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), numDatasets, c);
+              exposureTimes.put(numDatasets + "-" + c, new Time(exposureTime, UNITS.SECOND));
             }
           }
           catch (IndexOutOfBoundsException e) { }
@@ -878,14 +885,14 @@ else if (qName.equals("TimeStamp") && numDatasets >= 0) {
           store.setImageAcquisitionDate(new Timestamp(date), numDatasets);
         }
         firstStamp = ms;
-        store.setPlaneDeltaT(new Time(0.0, UNITS.SECOND), numDatasets, count);
+        deltaT.put(numDatasets + "-" + count, new Time(0.0, UNITS.SECOND));
       }
       else if (level != MetadataLevel.MINIMUM) {
         CoreMetadata coreMeta = core.get(numDatasets);
         int nImages = coreMeta.sizeZ * coreMeta.sizeT * coreMeta.sizeC;
         if (count < nImages) {
           ms -= firstStamp;
-          store.setPlaneDeltaT(new Time(ms / 1000.0, UNITS.SECOND), numDatasets, count);
+          deltaT.put(numDatasets + "-" + count, new Time(ms / 1000.0, UNITS.SECOND));
         }
       }
 
@@ -897,7 +904,8 @@ else if (qName.equals("RelTimeStamp") && level != MetadataLevel.MINIMUM) {
       if (count < nImages) {
         Double time = DataTools.parseDouble(attributes.getValue("Time"));
         if (time != null) {
-          store.setPlaneDeltaT(new Time(time, UNITS.SECOND), numDatasets, count++);
+          deltaT.put(numDatasets + "-" + count, new Time(time, UNITS.SECOND));
+          count++;
         }
       }
     }

diff --git a/components/formats-gpl/src/loci/formats/in/TCSReader.java b/components/formats-gpl/src/loci/formats/in/TCSReader.java
@@ -30,6 +30,7 @@
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import loci.common.DataTools;
 import loci.common.DateTools;
@@ -49,6 +50,7 @@
 import loci.formats.tiff.TiffParser;
 
 import ome.units.quantity.Length;
+import ome.units.quantity.Time;
 
 /**
  * TCSReader is the file format reader for Leica TCS TIFF files and their
@@ -465,6 +467,8 @@ else if (getSizeT() == 1) {
       else ms0.sizeZ *= ifds.size();
     }
 
+    Map<String, Time> exposureTime = null;
+    Map<String, Time> deltaT = null;
     if (xmlFile != null) {
       // parse XML metadata
 
@@ -474,6 +478,8 @@ else if (getSizeT() == 1) {
       LeicaHandler handler =
         new LeicaHandler(store, getMetadataOptions().getMetadataLevel());
       XMLTools.parseXML(xml, handler);
+      exposureTime = handler.getExposureTimes();
+      deltaT = handler.getDeltaT();
 
       metadata = handler.getGlobalMetadata();
       MetadataTools.merge(handler.getGlobalMetadata(), metadata, "");
@@ -509,6 +515,20 @@ else if (getSizeT() == 1) {
     if (sizeZ != null) {
       store.setPixelsPhysicalSizeZ(sizeZ, 0);
     }
+
+    for (int s=0; s<getSeriesCount(); s++) {
+      setSeries(s);
+      for (int i=0; i<getImageCount(); i++) {
+        String key = s + "-" + i;
+        if (exposureTime != null && exposureTime.containsKey(key)) {
+          store.setPlaneExposureTime(exposureTime.get(key), s, i);
+        }
+        if (deltaT != null && deltaT.containsKey(key)) {
+          store.setPlaneDeltaT(deltaT.get(key), s, i);
+        }
+      }
+    }
+    setSeries(0);
   }
 
   // -- Helper methods --