encoding bug in OpenJPEG third party module about itk HOT 6 OPEN

The version of OpenJPEG in ITK which is used for JPEG2000 compression (default codec when writing DICOM via GDCM)

GDCM uses own OpenJPEG library (or "system" optionally), it is libitkgdcmopenjp2-5.4.a in ITK build. Yes, it is rather old, 2.3.0 (from 2019, AFAIK). CC @malaterre

...
[ 37%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeFiles/gdcmopenjp2.dir/j2k.c.o
[ 37%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeFiles/gdcmopenjp2.dir/jp2.c.o
[ 37%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeFiles/gdcmopenjp2.dir/mct.c.o
[ 37%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeFiles/gdcmopenjp2.dir/mqc.c.o
[ 37%] Building C object Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeFiles/gdcmopenjp2.dir/openjpeg.c.o
...

from itk.

Is this an issue that need to be reported and addressed in the GDCM repo?

from itk.

Is this an issue that need to be reported and addressed in the GDCM repo?

GDCM uses own OpenJPEG library (or "system" optionally)

Yes, but also there may be other issues with BitsAllocated 32 sometimes and the line
prec=%u (should be between 1 and 38 according to the JPEG2000 norm. OpenJpeg only supports up to 31)
is still in OpenJpeg master, s. here and here. It is not simple, IMHO. Maybe build GDCM with system's OpenJpeg (on Linux it is easy and the version is 2.5.0+) and test, does it help or not.

Edit: also see this line in GDCM.

from itk.

Just posted the issue on the GDCM bug-tracker (https://sourceforge.net/p/gdcm/bugs/559/).

@malaterre, really appreciate your help resolving this. We have some naive SimpleITK users who encountered the problem, using a system OpenJPEG is not an option for them - it is beyond what they can do. Thanks.

from itk.

Just posted the issue on the GDCM bug-tracker (https://sourceforge.net/p/gdcm/bugs/559/).

@malaterre, really appreciate your help resolving this. We have some naive SimpleITK users who encountered the problem, using a system OpenJPEG is not an option for them - it is beyond what they can do. Thanks.

@zivy I was not involved in the original Modules/ThirdParty/OpenJPEG, please update and you should be done. Last I checked this is the j2k module used by ITK/GDCM.

from itk.

Hello @malaterre,

Sorry, but I'm a bit confused.

Per @issakomi's observation, the OpenJPEG library used by GDCM appears to be fromModules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg which is separate from the Modules/ThirdParty/OpenJPEG (I originally thought that module was what needed to be upgraded). This is why I ended up posting the request for updating the library on the gdcm issue tracker. What am I missing here? Thanks for taking a look at this.

from itk.