From ab8234f870221f6e56ddec8688a16de4d00f85e0 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 11 Sep 2024 11:59:00 -0500
Subject: [PATCH] Don't try to convert lengths with pixel/referenceframe units
 to physical units

---
 .../src/loci/formats/out/DicomWriter.java     | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/components/formats-bsd/src/loci/formats/out/DicomWriter.java b/components/formats-bsd/src/loci/formats/out/DicomWriter.java
index 4b26e2e8dc7..05d27e26de6 100644
--- a/components/formats-bsd/src/loci/formats/out/DicomWriter.java
+++ b/components/formats-bsd/src/loci/formats/out/DicomWriter.java
@@ -988,7 +988,7 @@ public void setId(String id) throws FormatException, IOException {
           opticalSequence.children.add(illuminationTypeCodes);
 
           DicomTag wavelength = new DicomTag(ILLUMINATION_WAVELENGTH, FL);
-          Length wave = r.getChannelEmissionWavelength(pyramid, c);
+          Length wave = fixUnits(r.getChannelEmissionWavelength(pyramid, c));
           wavelength.value = new float[] {wave == null ? 1f : wave.value(UNITS.NM).floatValue()};
           opticalSequence.children.add(wavelength);
 
@@ -1019,7 +1019,7 @@ public void setId(String id) throws FormatException, IOException {
 
         DicomTag sliceThickness = new DicomTag(SLICE_THICKNESS, DS);
         DicomTag sliceSpace = new DicomTag(SLICE_SPACING, DS);
-        Length physicalZ = r.getPixelsPhysicalSizeZ(pyramid);
+        Length physicalZ = fixUnits(r.getPixelsPhysicalSizeZ(pyramid));
         if (physicalZ != null) {
           sliceThickness.value = padString(String.valueOf(physicalZ.value(UNITS.MM)));
         }
@@ -1032,8 +1032,8 @@ public void setId(String id) throws FormatException, IOException {
         pixelMeasuresSequence.children.add(sliceSpace);
 
         DicomTag pixelSpacing = new DicomTag(PIXEL_SPACING, DS);
-        Length physicalX = r.getPixelsPhysicalSizeX(pyramid);
-        Length physicalY = r.getPixelsPhysicalSizeY(pyramid);
+        Length physicalX = fixUnits(r.getPixelsPhysicalSizeX(pyramid));
+        Length physicalY = fixUnits(r.getPixelsPhysicalSizeY(pyramid));
         String px = physicalX == null ? "1" : String.valueOf(physicalX.value(UNITS.MM));
         String py = physicalY == null ? "1" : String.valueOf(physicalY.value(UNITS.MM));
         pixelSpacing.value = padString(px + "\\" + py);
@@ -2076,6 +2076,18 @@ private short[] makeShortArray(int v) {
     return s;
   }
 
+  /**
+   * Check if the unit for the given Length is "pixel"
+   * or "referenceframe". These two units cannot be assigned to
+   * proper physical units (e.g. mm), so need to be handled specially.
+   */
+  private Length fixUnits(Length size) {
+    if (size == null || size.unit() == UNITS.PIXEL || size.unit() == UNITS.REFERENCEFRAME) {
+      return null;
+    }
+    return size;
+  }
+
   private TiffRational getPhysicalSize(Length size) {
     if (size == null || size.value(UNITS.MICROMETER) == null) {
       return new TiffRational(0, 1000);