PALETTE COLOR to RGB conversion

[SamJK001]

So, I am trying to decompress US images and have successfully managed to do so thanks to @scaramallion in #1583. This solution works perfectly for images in YBR_FULL or YBR_FULL_422 colour spaces. However, I have some images that have a PhotometricInterpretation value of PALETTE COLOR.

I am trying to use the apply_color_lut() function to convert to rgb. However, this does not work.

ds = dcmread(...)

if ds.file_meta.TransferSyntaxUID.is_compressed:
        arr = ds.pixel_array

        if ds.PhotometricInterpretation in ("PALETTE COLOR"):
               rgb = apply_color_lut(arr, ds)
        
        ds.PixelData = arr.tobytes()
        ds.file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
        ds.save_as(...)

Here are the group 0028 elements:

(Group,Elemnt)	TAG Description				VR	VM	Len	Value
(0028,0002)	SamplesPerPixel				US	1	2	1
(0028,0004)	PhotometricInterpretation		CS	1	14	PALETTE COLOR
(0028,0008)	NumberOfFrames				IS	1	2	29
(0028,0009)	FrameIncrementPointer			AT	1	4	(0018,1065)
(0028,0010)	Rows					US	1	2	600
(0028,0011)	Columns					US	1	2	800
(0028,0014)	UltrasoundColorDataPresent		US	1	2	1
(0028,0100)	BitsAllocated				US	1	2	16
(0028,0101)	BitsStored				US	1	2	16
(0028,0102)	HighBit					US	1	2	15
(0028,0103)	PixelRepresentation			US	1	2	0
(0028,1101)	RedPaletteColorLookupTableDescriptor	US	3	6	0\0\16
(0028,1102)	GreenPaletteColorLookupTableDescriptor	US	3	6	0\0\16
(0028,1103)	BluePaletteColorLookupTableDescriptor	US	3	6	0\0\16
(0028,1201)	RedPaletteColorLookupTableData		OW	1	131072	
(0028,1202)	GreenPaletteColorLookupTableData	OW	1	131072	
(0028,1203)	BluePaletteColorLookupTableData		OW	1	131072	
(0028,2110)	LossyImageCompression			CS	1	2	00

The image then renders in an incorrect colour space when saved.

I think it may be due to elements 1201-03 being either blank or stored as OW and not Bits, but I am not sure. Any suggestions?

Thanks!

[mrbean-bremen]

(ignore the first version of the reply, I misread the question)

The PaletteColorLookupTableData tags are of type OW, so this is correct, not sure what you mean by being them blank.

You don't show what you actually do with the returned rgb array, in your code it looks like you don't use it at all.
I assume that you change the colorspace to RGB and use the returned array as pixeldata. In your case, this probably won't work, because you get 16 bit data, meaning that the output will have each color component as an uint16. If you want to convert this into RGB, you have to downscale it to 8 bit first.

[scaramallion]

To clarify, the DICOM Standard says that an ultrasound that doesn't use a Photometric Interpretation of PALETTE COLOR should have Bits Stored of 8 for RGB pixel data.

I don't really understand why they allow a 16-bit LUT if that's the case.