Transcoding API ?

salimkanoun · November 14, 2018, 2:41pm

Hi there,

I have a question about DICOM Transcoding.
First of all my main problem : I’m using Orthanc to store images coming from different center, and it does the job perfectly. The data stored contains both regular and compressed DICOM.
Problem, at the end I want to read the image using Fiji which has a incomplete compressed DICOM support.
Since the data are important by Orthanc using original files, I can’t rely on a PACS decompression feature during the DICOM negociation.

I know that the problem is not simple.

I have several questions about this compressed DICOM :

I see there is a lua script to automatically compress DICOM (https://bitbucket.org/sjodogne/orthanc/src/89f2c302fc377044fd3963d73ccb31b31985bd40/Resources/Samples/Lua/AutomatedJpeg2kCompression.lua?at=default&fileviewer=file-view-default).
I guess there is a way to revert it and make uncompressed DICOMs.
The script call "os.execute('gdcmconv "
When Orthanc is started with the viewer plugin it rely on GDCM, is this os.execute could find the gdcmconv inside orthanc librairies or does it need an external install in the OS ?
When orthanc is used with GDCM is it feasible to expose the gdcmconv to a restAPI to make DICOM transcoding ? (so I guess in a Orthanc C plugin)
Eventually is there some trancoding APIs already available or planned that i’m not aware about ?

Best regards,

Salim

bdearlove · November 14, 2018, 3:40pm

Hi Salim,
Just to confirm, you are looking to compress when receiving the images and decompressing when sending to Fiji?

salimkanoun · November 14, 2018, 4:05pm

The most simple for me would be that all Orthanc is uncompressed, so that orthanc could automatically uncompress dicom that are sent compressed.

Or eventually make all orthanc output uncompressed, to read them to Fiji I ask Orthanc for a archive with the tool/archive API, ideally it would be that all outputed dicom comes uncompressed in the ZIP.

Best regard
s,
Salim

bdearlove · November 14, 2018, 5:02pm

I think setting the compressed transfer syntaxes to False and keep DeflatedTransferSyntaxAccepted to true in Orthanc config it should tell to send uncompressed to Orthanc. (At least does for me)

salimkanoun · November 15, 2018, 9:16am

Yes but only in case your get the dicom from a pacs that do the transcode for you.

On our project we import raw file with the instance post api

jodogne · September 3, 2019, 11:21am

Hello,

In order to clarify the status of transcoding in Orthanc, I’ve just added a new FAQ entry about this topic in the Orthanc Book:
https://book.orthanc-server.com/faq/transcoding.html

HTH,
Sébastien-