[Ctk-developers] DCMTK JPEG 2000 support (was: [slicer-devel] JPEG 2000)

Tue Feb 25 18:01:44 EST 2014

---------- Forwarded message ----------
From: Aaron Boxer <boxerab at gmail.com>
Date: Fri, Feb 21, 2014 at 3:28 PM
Subject: Re: [slicer-devel] JPEG 2000
To: "slicer-devel at bwh.harvard.edu" <slicer-devel at bwh.harvard.edu>

Well Folks, I've been able to successfully decode jpeg 2000 images on my
dcmtk branch.

You can find the branch here:

https://github.com/OpenRadStack/dcmtk/tree/j2k

I am still using git submodules and manual build to build openjpeg; haven't
had a chance yet to follow Jcr's build advice.

If you would like to try it out, you can follow these steps:

1) clone the project
2) run  $  git submodule init & git submodule update
3) use cmake to build  openjpeg  (third-party/openjpeg)   into
third-party/openjpeg-build   folder (enable shared library)
4) make sure that openjp2 shared library is in your path

For testing, I am running the dcmtk dcmj2pnm command line tool to convert
dicom images to bmp.

Command line I am using:

+ob +Wm dicomFile destinationFile.bmp

Cheers,
Aaron

On Thu, Feb 20, 2014 at 2:26 PM, Jean-Christophe Fillion-Robin <
jchris.fillionr at kitware.com> wrote:

> Hi Aaron,
>
> This is great news.
>
> I don't think DCMTK should use either git submodule or External project,
> instead you should assume the library is either installed on the system or
> related path passed at configure time. You could then just call:
>
>     find_package(OpenJPEG NO_MODULE)    See [1]
>
> in the 3rdparty.cmake. See [2]
>
> When configuring DCMTK, it means you would simply pass the path the
> OpenJPEG build tree passing -DOpenJPEG_DIR:PATH=/path/to/openJPEG-build
>
>
> [1] This is possible because a OpenJPEGConfig.cmake is configured. see
> http://code.google.com/p/openjpeg/source/browse/trunk/cmake/OpenJPEGConfig.cmake.inand
> http://code.google.com/p/openjpeg/source/browse/trunk/CMakeLists.txt#298
>
> [2] https://github.com/commontk/DCMTK/blob/patched-3/CMake/3rdparty.cmake
>
>
> On Thu, Feb 20, 2014 at 2:08 PM, Aaron Boxer <boxerab at gmail.com> wrote:
>
>> Update: I am closing in on a jpeg2000-enabled branch from DCMTK master.
>> Should be ready next week.
>> One issue I am having: I have added the openjpeg project (which is a
>> cmake proj) to dcmtk as a git submodule.
>> Now I need to figure out how the cmake externalproject command works.
>>
>> (
>> http://www.cmake.org/cmake/help/v2.8.12/cmake.html#module:ExternalProject
>> )
>>
>> If anyone here is familiar with this, and would like to help, please let
>> me know.
>>
>> Thanks,
>> Aaron
>>
>>
>>
>> On Mon, Feb 17, 2014 at 9:45 AM, Steve Pieper <pieper at isomics.com> wrote:
>>
>>> Hi Aaron -
>>>
>>> I like your plan of reviewing the osirix implementation and taking
>>> advantage of the latest developments in OpenJPEG - very exciting to see
>>> this moving ahead!
>>>
>>> Regarding your questions about thumbnails in ctkDICOM2: CTK only uses
>>> DCMTK, not GDCM, so it currently fails to create thumbnails for images not
>>> directly supported by DCMTK.  CTK doesn't have a mechanism to use ITK or
>>> GDCM, although I suppose this could be added.  In ctk we really wanted to
>>> have robust networking support in CTK and as you noted DCMTK has a well
>>> established track record in this.
>>>
>>> Best,
>>> Steve
>>>
>>>
>>> On Mon, Feb 17, 2014 at 8:53 AM, Aaron Boxer <boxerab at gmail.com> wrote:
>>>
>>>> Hi Steve,
>>>>
>>>>
>>>>> That would be an awesome contribution - useful for slicer but also for
>>>>> CTK and other DCMTK users.  The situation right now is that slicer builds
>>>>> dcmtk (without jpeg2000 as you noted) so none of the dcmtk-based code can
>>>>> access that kind of image.  So for example in the ctkDICOM app the
>>>>> thumbnails aren't displayed for data of that type.  The osirix sample data
>>>>> is a good source of images that are compressed in a way dcmtk doesn't like.
>>>>>
>>>>> That said, when slicer actually goes to read the data it is delegated
>>>>> to ITK's readers, which include GDCM and that supports jpeg2000 so the
>>>>> files load.
>>>>>
>>>>
>>>>  Interesting. Can the ctkDICOM app use GDCM for the thumbnails?
>>>>
>>>>
>>>>>
>>>>> This is an oddly messy situation.  Personally I wish ITK had used
>>>>> DCMTK from the start, since that includes all the networking and other
>>>>> support.  But instead it started with GDCM, on the idea that it's lighter
>>>>> weight and has support for things like jpeg2000 and then later added DCMTK
>>>>> support too.  Since slicer delegates to ITK, there are some situations
>>>>> where DCMTK is used and others where GDCM is used.
>>>>>
>>>>
>>>>  Yes. GDCM and DCMTK seem to excell in orthogonal areas: GDCM on DICOM
>>>> image reading and DCMTK on DICOM networking. So, I can see why ITK chose
>>>> GDCM initially, because it is an image-focused toolkit.
>>>>
>>>> I would like to see more networking in GDCM, and more transfer syntaxes
>>>> supported in the open DCMTK version :)
>>>>
>>>> Anywho, I would be happy to add both JPEG2000 and JPEG-LS to DCMTK.
>>>>
>>>> Cheers,
>>>> Aaron
>>>>
>>>>
>>>>
>>>>
>>>>>
>>>>> On Sat, Feb 15, 2014 at 10:05 AM, Aaron Boxer <boxerab at gmail.com>wrote:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I was wondering about types of compression supported by the slicer
>>>>>> DICOM module.
>>>>>> As you probably know, many DICOM images are compressed with JPEG 2000
>>>>>> compression. And I believe that DCMTK sells support for JPEG 2000, which
>>>>>> leads me to believe that the slicer version of DCMTK does not support JPEG
>>>>>> 2000.
>>>>>>
>>>>>> Is this the case? Because I have done some work on the OpenJPEG
>>>>>> project, and I think I could integrate OpenJPEG support into the slicer
>>>>>> DCMTK.
>>>>>>
>>>>>> Kind Regards,
>>>>>> Aaron
>>>>>>
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