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Don't alter OME-XML BigEndian values for int8/uint8 data #151

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Don't alter OME-XML BigEndian values for int8/uint8 data #151

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57d0184
Don't alter OME-XML BigEndian values for int8/uint8 data
melissalinkert Mar 9, 2026
c6699e1
Merge branch 'master' of github.com:glencoesoftware/raw2ometiff into …
melissalinkert Apr 9, 2026
3ae41d0
Handle v2 big endian data types
melissalinkert Apr 9, 2026
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26 changes: 21 additions & 5 deletions src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -881,18 +881,24 @@ private PixelType getPixelType(dev.zarr.zarrjava.v2.DataType type) {
case INT8:
return PixelType.INT8;
case INT16:
case INT16_BE:
return PixelType.INT16;
case INT32:
case INT32_BE:
return PixelType.INT32;
case UINT8:
return PixelType.UINT8;
case UINT16:
case UINT16_BE:
return PixelType.UINT16;
case UINT32:
case UINT32_BE:
return PixelType.UINT32;
case FLOAT32:
case FLOAT32_BE:
return PixelType.FLOAT;
case FLOAT64:
case FLOAT64_BE:
return PixelType.DOUBLE;
default:
throw new IllegalArgumentException("Unsupported pixel type: " + type);
Expand Down Expand Up @@ -1289,10 +1295,20 @@ else if (s.c < dims[channelIndex]) {
s.planeCount = s.z * s.t;

// Zarr format allows both little and big endian order
s.littleEndian = !bigEndian;
if (bigEndian != metadata.getPixelsBigEndian(seriesIndex)) {
LOG.debug("Setting BigEndian={} for series {}", bigEndian, seriesIndex);
metadata.setPixelsBigEndian(bigEndian, seriesIndex);
// respect OME-XML for int8/uint8 data, but the Zarr metadata otherwise
// this prevents false mismatches for OME-XML that has the same
// BigEndian value for every Image, but a mix of int8/uint8 and other
// PixelTypes
if (type != PixelType.INT8 && type != PixelType.UINT8) {
s.littleEndian = !bigEndian;
if (bigEndian != metadata.getPixelsBigEndian(seriesIndex)) {
LOG.warn("Setting BigEndian={} for series {}",
bigEndian, seriesIndex);
metadata.setPixelsBigEndian(bigEndian, seriesIndex);
}
}
else {
s.littleEndian = !metadata.getPixelsBigEndian(seriesIndex);
}

// make sure pixel types are consistent between Zarr and OME metadata
Expand All @@ -1308,7 +1324,7 @@ else if (s.c < dims[channelIndex]) {
if (seriesIndex > 0 && s.littleEndian != series.get(0).littleEndian) {
// always warn on endian mismatches
// mismatch is only fatal if pixel type is neither INT8 nor UINT8
String msg = String.format("Endian mismatch in series {} (expected {}",
String msg = String.format("Endian mismatch in series %d (expected %s)",
seriesIndex, series.get(0).littleEndian);
if (FormatTools.getBytesPerPixel(s.pixelType) > 1) {
throw new FormatException(msg);
Expand Down
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