Merge pull request #4215 from melissalinkert/fix-dicom-export-imagej

Fix DICOM export in ImageJ
ome · Sep 13, 2024 · e431517 · e431517
2 parents 1f03e09 + c7e9161
commit e431517
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Showing 2 changed files with 27 additions and 5 deletions.
diff --git a/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java b/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java
@@ -505,7 +505,7 @@ else if (FormatTools.isSigned(originalType)) {
                     String lsid = MetadataTools.createLSID("Channel", 0, c);
                     store.setChannelID(lsid, 0, c);
                 }
-                store.setChannelSamplesPerPixel(new PositiveInteger(channels), 0, 0);
+                store.setChannelSamplesPerPixel(new PositiveInteger(channels), 0, c);
 
                 if (imp instanceof CompositeImage) {
                     luts[c] = ((CompositeImage) imp).getChannelLut(c + 1);

diff --git 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);
@@ -1383,6 +1383,11 @@ public void close() throws IOException {
         for (int res=0; res<resolutionCount; res++) {
           resolution = res;
           openFile(pyramid, resolution);
+
+          if (out == null) {
+            // already closed
+            continue;
+          }
           int resolutionIndex = getIndex(pyramid, resolution);
 
           out.seek(out.length());
@@ -2071,6 +2076,23 @@ 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) {
+      return null;
+    }
+    if (size.unit() == UNITS.PIXEL || size.unit() == UNITS.REFERENCEFRAME) {
+      LOGGER.warn("Found physical length '{}' in relative units '{}'; this value will be lost",
+        size.value(), size.unit());
+      return null;
+    }
+    return size;
+  }
+
   private TiffRational getPhysicalSize(Length size) {
     if (size == null || size.value(UNITS.MICROMETER) == null) {
       return new TiffRational(0, 1000);