Read and write spacing and zunit ImageJ TIFF metadata

melissalinkert · Sep 20, 2024 · 41858b0 · 41858b0
1 parent 686371d
commit 41858b0
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Showing 2 changed files with 19 additions and 4 deletions.
diff --git a/components/formats-bsd/src/loci/formats/in/TiffReader.java b/components/formats-bsd/src/loci/formats/in/TiffReader.java
@@ -82,6 +82,7 @@ public class TiffReader extends BaseTiffReader {
   private String companionFile;
   private String description;
   private String calibrationUnit;
+  private String zUnit;
   private Double physicalSizeZ;
   private Time timeIncrement;
   private Integer xOrigin, yOrigin;
@@ -113,6 +114,7 @@ public void close(boolean fileOnly) throws IOException {
       companionFile = null;
       description = null;
       calibrationUnit = null;
+      zUnit = null;
       physicalSizeZ = null;
       timeIncrement = null;
       xOrigin = null;
@@ -137,6 +139,7 @@ protected void initStandardMetadata() throws FormatException, IOException {
 
     description = null;
     calibrationUnit = null;
+    zUnit = null;
     physicalSizeZ = null;
     timeIncrement = null;
     xOrigin = null;
@@ -293,6 +296,10 @@ else if (token.startsWith("unit=")) {
         calibrationUnit = value;
         put("Unit", calibrationUnit);
       }
+      else if (token.startsWith("zunit=")) {
+        zUnit = value;
+        put("Z Unit", zUnit);
+      }
       else if (token.startsWith("finterval=")) {
         Double valueDouble = parseDouble(value);
         if (valueDouble != null) {
@@ -404,7 +411,7 @@ private void populateMetadataStoreImageJ(MetadataStore store) {
     if (physicalSizeZ != null) {
       double zDepth = physicalSizeZ.doubleValue();
       if (zDepth < 0) zDepth = -zDepth;
-      Length z = FormatTools.getPhysicalSizeZ(zDepth);
+      Length z = FormatTools.getPhysicalSizeZ(zDepth, zUnit);
       if (z != null) {
         store.setPixelsPhysicalSizeZ(z, 0);
       }

diff --git a/components/formats-bsd/src/loci/formats/out/TiffWriter.java b/components/formats-bsd/src/loci/formats/out/TiffWriter.java
@@ -484,9 +484,17 @@ else if (retrieve.getPixelsBinDataCount(series) == 0) {
     int channels = retrieve.getPixelsSizeC(series).getValue().intValue();
     int z = retrieve.getPixelsSizeZ(series).getValue().intValue();
     int t = retrieve.getPixelsSizeT(series).getValue().intValue();
-    ifd.putIFDValue(IFD.IMAGE_DESCRIPTION,
-      "ImageJ=\nhyperstack=true\nimages=" + (channels * z * t) + "\nchannels=" +
-      channels + "\nslices=" + z + "\nframes=" + t);
+
+    String imagejMetadata = "ImageJ=\nhyperstack=true\nimages=" +
+      (channels * z * t) + "\nchannels=" +
+      channels + "\nslices=" + z + "\nframes=" + t;
+    Length physicalSizeZ = retrieve.getPixelsPhysicalSizeZ(series);
+    if (physicalSizeZ != null) {
+      Double zSpacing = physicalSizeZ.value().doubleValue();
+      String zUnit = physicalSizeZ.unit().getSymbol();
+      imagejMetadata += "\nzunit=" + zUnit + "\nspacing=" + zSpacing;
+    }
+    ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, imagejMetadata);
 
     int index = (no * getResolutionCount()) + getResolution();
     int currentSeries = getSeries();