Incorrect image when decoding multiframe pixeldata

[thomas-tribus]

I've noticed that pixeldata is decoded incorrectly when using decode_pixel_data() and then exporting individual frames. When exporting using decode_pixel_data_frame I get correct results. I'm using 2D ultrasound with ybr_full_422 photometric interpretation.

So this works:

let frame = 0;
let pix = dicom.decode_pixel_data_frame(frame)?;
let img_data = pix.to_dynamic_image(0)?;
img_data.save("out.png")?;

And this doesn't:

let frame = 0;
let pixel_data = dicom.decode_pixel_data()?;
//The colors in the output are wrong
let img_data = pixel_data.to_dynamic_image(frame)?;
img_data.save("out.png")?;

Correct result:

Result when decoding all frames:

I've found a likely culprit too, when using decode_pixel_data a new photometric interpretation is computed based on the number of channels in the input image (see below). The single frame decode_pixel_data_frame doesn't have this (seemingly incorrect) transformation.

// pixels are already interpreted,
// set new photometric interpretation
let new_pi = match samples_per_pixel {
    1 => PhotometricInterpretation::Monochrome2,
    3 => PhotometricInterpretation::Rgb,
    _ => photometric_interpretation,
};

I've created a PR that removes the code and that seems to fix the issue.

[thomas-tribus]

PR: #562

It seems I can't link it in the development panel, so here it is in the comments.

[Enet4]

Thank you for reporting. Seeing #562, this seems to be specific to the GDCM integration, correct? Is the ultrasound in JPEG baseline?

[thomas-tribus]

Tbh, I only tested with the GDCM implementation. And you are right, the ultra sound is in JPEG baseline: Transfer Syntax: 1.2.840.10008.1.2.4.50 (JPEG Baseline (Process 1))

From dicom-dump (some tags omitted):

Media Storage SOP Class UID: 1.2.840.10008.5.1.4.1.1.3.1 (Ultrasound Multi-frame Image Storage)
Media Storage SOP Instance UID: 1.2.840.113619.2.118.541852079.1603983996.11.7.512
Transfer Syntax: 1.2.840.10008.1.2.4.50 (JPEG Baseline (Process 1))
Implementation Class UID: 1.2.840.113619.6.118
Implementation version name: ECHOPAC_201
Source Application Entity Title: VIVIDS70-000384

----------------------------------------------------------
(0008,0008) ImageType                    CS (4, 22 bytes): ["DERIVED", "PRIMARY", "", "0011"]
(0008,0016) SOPClassUID                  UI (1, 28 bytes): "1.2.840.10008.5.1.4.1.1.3.1"
(0008,0018) SOPInstanceUID               UI (1, 50 bytes): "1.2.840.113619.2.118.541852079.1603983996.11.7.512"
(0008,0070) Manufacturer                 LO (1, 24 bytes): "GE Healthcare Ultrasound"
(0008,1090) ManufacturerModelName        LO (1, 10 bytes): "Vivid S70"
(0008,2142) StartTrim                    IS (1,  2 bytes): "1"
(0008,2143) StopTrim                     IS (1,  2 bytes): "18"
(0008,2144) RecommendedDisplayFrameRate  IS (1,  2 bytes): "13"
(0018,0040) CineRate                     IS (1,  2 bytes): "13"
(0018,0072) EffectiveDuration            DS (1,  4 bytes): "1.27"
(0018,1020) SoftwareVersions             LO (1, 18 bytes): "Vivid S70:201.84.0"
(0018,1063) FrameTime                    DS (1,  8 bytes): "74.7059"
(0018,1066) FrameDelay                   DS (1,  2 bytes): "0"
(0018,1088) HeartRate                    IS (1,  2 bytes): "95"
(0018,1242) ActualFrameDuration          IS (1,  2 bytes): "74"
(0018,1244) PreferredPlaybackSequencing  US (1,  2 bytes): 0
(0018,6060) RWaveTimeVector              FL (3, 12 bytes): [15.934, 659.238, 1113.335]
(0028,0002) SamplesPerPixel              US (1,  2 bytes): 3
(0028,0004) PhotometricInterpretation    CS (1, 12 bytes): "YBR_FULL_422"
(0028,0006) PlanarConfiguration          US (1,  2 bytes): 0
(0028,0008) NumberOfFrames               IS (1,  2 bytes): "18"
(0028,0009) FrameIncrementPointer        AT (1,  4 bytes): (0018,1063)
(0028,0010) Rows                         US (1,  2 bytes): 708
(0028,0011) Columns                      US (1,  2 bytes): 1016
(0028,0014) UltrasoundColorDataPresent   US (1,  2 bytes): 1
(0028,0100) BitsAllocated                US (1,  2 bytes): 8
(0028,0101) BitsStored                   US (1,  2 bytes): 8
(0028,0102) HighBit                      US (1,  2 bytes): 7
(0028,0103) PixelRepresentation          US (1,  2 bytes): 0
(0028,2110) LossyImageCompression        CS (1,  2 bytes): "01"
(0028,2112) LossyImageCompressionRatio   DS (1,  2 bytes): "95"
(7FE0,0010) PixelData                    OB (PixelSequence, 19 Items)