Open jcupitt opened 6 months ago
Also, even with -precompressed
, bfconvert
re-encodes the label and overview images to YCbCr but leaves their PhotometricInterpretation values as RGB.
Thanks for reporting this, @jcupitt / @bgilbert. Just to make sure I understand before implementing a fix, is the following what you would expect to be sufficient:
PhotometricInterpretation
(i.e 0x0028,0004
) needs to be changed-precompressed
was used, and no re-encoding was performed, then PhotometricInterpretation
should be RGB
-compression JPEG
was used, and either -precompressed
was used but re-encoding needed to happen anyway or -precompressed
was not used, then PhotometricInterpretation
should be YBR_FULL_422
-compression
was omitted or set to something other than JPEG
, then PhotometricInterpretation
should be RGB
PhotometricInterpretation
should remain MONOCHROME2
/cc @dclunie, @fedorov
Hi @melissalinkert, thanks for working on this.
I think you can assume the input file is correct, so if you just copy over the JPEG images, you don't need to do anything.
If you do a decompress or compress, you need to look at and perhaps set the DICOM photometricinterpretation tag.
Hello everyone, thank you for this nice thing.
While working on openslide, I've come across a
bfconvert
bug when generating DICOM files.DICOM has a photometricinterpretation tag to indicate either RGB or YCbCr colorspace in tiles. This (according to the DICOM spec) is the place where the tile colourspace is kept, and NOT in the JPEG tiles themselves. On decode, you need to open each tile, and force the tile colorspace from the DICOM header.
If you use
-precompressed
, conversion will copy over the JPEG tiles untouched, so if the DICOM header and the tile colorspace were correct beforehand, they will still match in the converted image.If you convert without the
precompressed
flag,bfconvert
will reencode the JPEGs and may well change the photometric interpretation. For example, SVS is saved as RGB (no chroma subsample), butbfconvert
will save as YCbCr (chroma subsample). Now the DICOM photometric interpretation will be RGB, but the tiles will be YCbCr, so users will see crazy colors.tldr: when saving DICOM, if tiles are being recompressed,
bfconvert
needs to update the DICOM photometric interpretation tag.Referring openslide issue: https://github.com/openslide/openslide/pull/558
Referring libdicom issue: https://github.com/ImagingDataCommons/libdicom/issues/80