Merge pull request #1966 from dgault/metamorph_voxelsize

Incorrect VoxelSize in MetaMorph Reader
ome · Sep 30, 2015 · 134c310 · 134c310
2 parents e5fa891 + d8f1f6e
commit 134c310
Showing 1 changed file with 33 additions and 0 deletions.
diff --git a/components/formats-gpl/src/loci/formats/in/MetamorphReader.java b/components/formats-gpl/src/loci/formats/in/MetamorphReader.java
@@ -27,6 +27,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.math.BigDecimal;
 import java.text.DecimalFormatSymbols;
 import java.util.Arrays;
 import java.util.ArrayList;
@@ -778,6 +779,38 @@ else if (differentZs) {
       if (zDistances != null) {
         stepSize = zDistances[0];
       }
+      else {
+        Vector<Double> zPositions = new Vector<Double>();
+        Vector<Double> uniqueZ = new Vector<Double>();
+
+        for (IFD ifd : ifds) {
+          MetamorphHandler zPlaneHandler = new MetamorphHandler();
+
+          String zComment = ifd.getComment();
+          if (zComment != null &&
+              zComment.startsWith("<MetaData>"))
+          {
+            try {
+              XMLTools.parseXML(XMLTools.sanitizeXML(zComment),
+                  zPlaneHandler);
+            }
+            catch (IOException e) { }
+          }
+
+          zPositions = zPlaneHandler.getZPositions();
+          for (Double z : zPositions) {
+            if (!uniqueZ.contains(z)) uniqueZ.add(z);
+          }
+        } 
+        if (uniqueZ.size() > 1 && uniqueZ.size() == getSizeZ()) {
+          BigDecimal lastZ = BigDecimal.valueOf(uniqueZ.get(uniqueZ.size() - 1));
+          BigDecimal firstZ = BigDecimal.valueOf(uniqueZ.get(0));
+          BigDecimal zRange = (lastZ.subtract(firstZ)).abs();
+          BigDecimal zSize = BigDecimal.valueOf((double)(getSizeZ() - 1));
+          stepSize = zRange.divide(zSize).doubleValue();
+        }
+      }
+
       Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
       if (physicalSizeZ != null) {
         store.setPixelsPhysicalSizeZ(physicalSizeZ, i);