RLE Lossless Encoding

The requirements for RLE encoding are defined in Section 8.2.2 and Annexes A.4.2 and G of Part 5 of the DICOM Standard. The underlying algorithm is based on the PackBits compression scheme.

Valid Image Pixel Parameters

The table below lists the valid Image Pixel module parameters for Pixel Data encoded using the RLE Lossless transfer syntax. For an explanation of each parameter and its relationship with the Pixel Data see the glossary of Image Pixel elements.

Samples per Pixel	Photometric Interpretation	Pixel Representation	Bits Allocated	Bits Stored
1	MONOCHROME1	0 or 1	8 or 16	1 to 16
	MONOCHROME2
	PALETTE COLOR	0
3	RGB	0	8 or 16	1 to 16
	YBR_FULL		8	1 to 8

To ensure you have the correct Photometric Interpretation when encoding using RLE Lossless, the uncompressed pixel data should already be in the corresponding color space:

• If your uncompressed pixel data is grayscale (intensity) based:

  • Use MONOCHROME1 if the minimum intensity value should be displayed as white.

  • Use MONOCHROME2 if the minimum intensity value should be displayed as black.

• If your uncompressed pixel data uses a single sample per pixel and is an index to the Red, Green and Blue Palette Color Lookup Tables:

  • Use PALETTE COLOR.

• If your uncompressed pixel data is in RGB color space:

  • For Photometric Interpretation RGB nothing else is required.

  • For Photometric Interpretation YBR_FULL

    • For Bits Allocated and Bits Stored less than or equal to 8: pixel data must be converted into YCbCr color space. However you should keep in mind that the conversion operation is lossy.

    • For Bits Allocated and Bits Stored between 9 and 16 (inclusive): pixel data should be downscaled to 8-bit (with Bits Stored, Bits Allocated and High Bit updated accordingly) and converted to YCbCr color space. Both of these operations are lossy.

• If your uncompressed pixel data is in YCbCr color space:

  • For Photometric Interpretation RGB the pixel data must first be converted into RGB color space. However the conversion operation is lossy.

  • For Photometric Interpretation YBR_FULL nothing else is required.

If a change is made to existing Pixel Data, such as conversion to a different color space or downsampling to 8-bit then a new SOP Instance UID should be generated.

You might be asking why you would convert uncompressed RGB pixel data to YCbCr (or vice versa) if the conversion itself is lossy. The answer is that using YCbCr data should result in a higher compression ratio than with RGB, while YCbCr data is usually converted back to RGB before viewing. The decision to change the color space should be made with the intended usage of your dataset in mind.

Available Plugins

Encoder	Plugins
	Name	Requires	Added	Known Limitations
RLELosslessEncoder	pydicom		v2.2	~20x slower to encode
	pylibjpeg	NumPy, pylibjpeg, pylibjpeg-rle	v2.2
	gdcm	GDCM	v2.2

Examples

Compressing grayscale pixel data in-place:

>>> from pydicom import examples
>>> from pydicom.uid import RLELossless
>>> ds = examples.ct
>>> ds.SamplesPerPixel
1
>>> ds.PhotometricInterpretation
'MONOCHROME2'
>>> ds.BitsAllocated
16
>>> ds.PixelRepresentation
1
>>> ds.compress(RLELossless)

Compressing RGB pixel data in-place:

>>> from pydicom import examples
>>> ds = examples.rgb_color
>>> ds.SamplesPerPixel
3
>>> ds.PhotometricInterpretation
'RGB'
>>> ds.BitsAllocated
8
>>> ds.PixelRepresentation
0
>>> len(ds.PixelData)
921600
>>> ds.compress(RLELossless)
>>> len(ds.PixelData)
424152

Convert RGB pixel data to YCbCr (requires NumPy), then compress in-place. Because the color space has changed we need to generate a new SOP Instance UID:

>>> from pydicom import examples
>>> from pydicom.pixels import convert_color_space
>>> from pydicom.uid import generate_uid
>>> ds = examples.rgb_color
>>> rgb = ds.pixel_array
>>> ybr = convert_color_space(rgb, 'RGB', 'YBR_FULL')
>>> ds.PhotometricInterpretation = 'YBR_FULL'
>>> ds.compress(RLELossless, ybr)
>>> ds.SOPInstanceUID = generate_uid()
>>> len(ds.PixelData)
187460