CODEWITHSUNDEEP
jpegdicom
korejwa
korejwa

Reputation: 61

Decoding lossless jpeg in nema.org DICOM files

I wrote a jpeg compressor/decompressor years ago, which can handle lossless and lossy jpeg files. It works well, but doesn't always decode jpeg streams in DICOM files correctly.

I know jpeg well, but I know little about DICOM. Lossless jpeg in DICOM can't possibly be compliant with the jpeg ISO standard. There must be some modification, either hard coded, or modified by a parameter somewhere in a DICOM file outside of the jpeg file stream.

My code fails on most of the sample DICOM files (compsamples_jpeg.tar) at: ftp://medical.nema.org/MEDICAL/Dicom/DataSets/WG04/

Here's what happens when I decode the first lossless jpeg (IMAGES\JPLL\CT1_JPLL) in this set:

dicom decoded image

The left image is rendered from my code, the right was rendered by an online DICOM reader: www (dot) ofoct (dot) com (slash) viewer (slash) dicom-viewer-online (dot) html

(x)MedCon, an open source DICOM reader, fails at the exact same pixel as my code, so I'm not the only one who has this problem. xmedcon dot sourceforge dot net

I have read this jpeg stream byte by byte, drew the huffman tree and calculated the huffman codes with pencil and paper, and my code does exactly what it is supposed to do. Here are the huffman codes:

Here is the compressed data after the SOS marker:

The online viewer says the first pixel value is -3024. If this is correct, the first diff value should be -3024, but it is not.

After this, my code correctly decodes about 2/5 of the image, but then decodes a wildly inaccurate diff value:

If you look at the image decoded by the online viewer, there is no radical change in pixel intensity at this location, so the si=11 value can't be correct.

I am sure I have a good understanding of jpeg, but jpeg streams in DICOM don't seem to follow the jpeg standard. What extensions/changes are made to jpeg streams when they are embedded in DICOM files?

Upvotes: 6

Views: 1147

Answers (2)

David Clunie
David Clunie

Reputation: 181

DICOM specifies the use of ISO 10918 just as it is written, so there is nothing magic about the use of lossless JPEG in DICOM images, other than the matters of reinterpreting the always unsigned output of the decoded bitstream as signed (depending on Pixel Representation) and applying the Rescale Slope and Intercept to the decoded "stored pixel values" into whatever "values" a viewer might report (e.g., as Hounsfield Units), as Paolo describes. Or to put it another way, do not rely on the "pixel values" reported by a viewer to be the same as the direct output of the decoded bitstream.

For reference, here are the sections in DICOM that address the use of 10918 in general:

http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_8.2.html#sect_8.2.1 http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_A.4.html#sect_A.4.1

DICOM encoders may split individual compressed frames into separate fragments, as in the case of this sample that deliberately uses fragmentation to test the decoding capability. I expect you know that and have taken care of reassembling compressed the bit stream across fragment boundaries (i.e., removing the fixed length Item tags between fragments):

http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_A.4.html

Though some encoders may be buggy, I don't think that is the case for IMAGES\JPLL\CT1_JPLL in the NEMA sample dataset, which I created many years ago using the Stanford PVRG codec.

My own decoder (minimal as it is) at http://www.dclunie.com/pixelmed/software/codec/ has no problem with it. The source is available, so if you want to recompile it with some of the debugging messages turned on to track each decoded value, predictor input value, restart at the beginning of each row, etc., to compare with your own logic, feel free.

Finally, since JPEG lossless is used rarely outside DICOM, you may find it hard to obtain other samples to test with. One such source that comes to mind is the USF digitized mammography collection (medical, but not DICOM), at http://marathon.csee.usf.edu/Mammography/Database.html.

David

PS. I did check which codec XMedCon is using at https://sourceforge.net/projects/xmedcon/ and it seems to use some copy of the Cornell lossless code; so it may be vulnerable to the same bug described in the post that BitBank referred to (https://groups.google.com/forum/#!topic/comp.protocols.dicom/Yl5GkZ8ggOE) or some other error. I didn't try to decipher the source code to see.

Upvotes: 6

Paolo Brandoli
Paolo Brandoli

Reputation: 4750

The first pixel's value is indeed -3024 as the online dicom viewer says:

You correctly decode the first amplitude as 30768, but the first pixel has the predictor set to zero and therefore its real value is 32768+30768=63536. This is an unsigned value.

Now, the pixel representation tag says that the file values are in b2 complement (signed), therefore when we use the most significant bit as a sign the value becomes -2000.

When we apply the value in the rescale slope intercept tag (-1024) then the value of the first pixel becomes -3024.

However, my codec doesn't find any amplitude 2047 near the row 179, so maybe your codec is going out of sync somehow: the loss of sync is also visible in the subsequent rows (they are all shifted to the right).

Upvotes: 2

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