Search found 17 matches

by samee
Wed, 2024-01-31, 14:35
Forum: DCMTK - Installation
Topic: Error building DCMTK with Apple M1 chip
Replies: 2
Views: 1187

Re: Error building DCMTK with Apple M1 chip

Hi Marco, I think the issue is coming from `CMake/3rdparty.cmake` file where we use `TIFF_LIBRARY` and `JPEG_LIBRARY` values. On the CMake side, these are actually `TIFF_LIBRARIES` and `JPEG_LIBRARIES`. After that modification, I was able to resolve the linking issue. I opened a PR in the GitHub rep...
by samee
Mon, 2024-01-29, 22:41
Forum: DCMTK - Installation
Topic: Error building DCMTK with Apple M1 chip
Replies: 2
Views: 1187

Error building DCMTK with Apple M1 chip

Hi there, I am a maintainer of an open-source feature extraction library for biomedical images that uses dcmtk to read dicom images. Till now, we have been using version 3.6.7 and were successfully able to integrate it to Windows, Linux and Apple Amd64 Python wheels. Now we are looking into creating...
by samee
Thu, 2023-05-04, 03:16
Forum: Third-Party DCMTK Applications
Topic: DICOM support for Nyxus - a feature extraction library
Replies: 0
Views: 98769

DICOM support for Nyxus - a feature extraction library

Hi everyone, Just wanted to share that we have added Dicom image processing support in our highly scalable library for calculating features from intensity-label image data ( https://github.com/PolusAI/nyxus ). I want to thank the volunteers for helping me out with question regarding using DCMTK API....
by samee
Wed, 2023-04-12, 19:35
Forum: DCMTK - Installation
Topic: CMAKE Options for Building Select Set of Modules
Replies: 2
Views: 10774

CMAKE Options for Building Select Set of Modules

Hi there,

My application only uses a select set of DCMTK modules: ofstd, oflog, dcmdata, dcmimgle, dcmimage, dcmjpeg, dcmjpls.

Is there a way to just build those (and preferably without the tests) using CMake?

Thanks,
Samee
by samee
Wed, 2023-04-12, 00:15
Forum: DCMTK - Installation
Topic: Correct Way to Include DCMTK in CMakeLists.txt
Replies: 3
Views: 10894

Re: Correct Way to Include DCMTK in CMakeLists.txt

Thanks for the reply. I did few more google search and what I understand is this behavior is due to the difference between how direct and indirect dependencies are resolved (at least in Linux). Here is a link that discusses this: https://stackoverflow.com/questions/52018092/how-to-set-rpath-and-runp...
by samee
Tue, 2023-04-11, 21:53
Forum: DCMTK - Installation
Topic: Correct Way to Include DCMTK in CMakeLists.txt
Replies: 3
Views: 10894

Re: Correct Way to Include DCMTK in CMakeLists.txt

Few updates. I reordered the link_directories() and add_executable() calls and the linking error is gone. However, now I get the following error: ./dicom_reader: error while loading shared libraries: liboflog.so.17: cannot open shared object file: No such file or directory using ldd shows the the fo...
by samee
Tue, 2023-04-11, 21:42
Forum: DCMTK - Installation
Topic: Correct Way to Include DCMTK in CMakeLists.txt
Replies: 3
Views: 10894

Correct Way to Include DCMTK in CMakeLists.txt

I am getting a linking error like the following while trying to add DCMTK to my project. [100%] Linking CXX executable dicom_reader /usr/bin/ld: cannot find -lofstd /usr/bin/ld: cannot find -loflog /usr/bin/ld: cannot find -ldcmdata /usr/bin/ld: cannot find -li2d /usr/bin/ld: cannot find -ldcmimgle ...
by samee
Tue, 2023-04-11, 19:44
Forum: DCMTK - Installation
Topic: dcmtk Conda package
Replies: 2
Views: 9997

Re: dcmtk Conda package

Thanks for the reply.

I finally found that the package has been moved from the bioconda channel to conda-forge channel https://anaconda.org/conda-forge/dcmtk.

-Samee
by samee
Fri, 2023-04-07, 16:07
Forum: DCMTK - Installation
Topic: dcmtk Conda package
Replies: 2
Views: 9997

dcmtk Conda package

Hi, Do the dcmtk developers/maintainers officially produce a conda package? I see that the bioconda channel has a dcmtk package https://anaconda.org/bioconda/dcmtk/ . But this is an old version (3.6.1), even though the tag says 3.6.7. Also, what is confusing is that the official bioconda page does n...
by samee
Wed, 2023-04-05, 21:04
Forum: DCMTK - General
Topic: How to Read Pixel Data when Pixel Representation=1
Replies: 6
Views: 5681

Re: How to Read Pixel Data when Pixel Representation=1

I think I have figured out the issue. I needed to register the codecs to be able to read the compressed image. Adding the following lines before everything seems to work. DJDecoderRegistration::registerCodecs(); DJLSDecoderRegistration::registerCodecs(); DcmRLEDecoderRegistration::registerCodecs();
by samee
Wed, 2023-04-05, 14:40
Forum: DCMTK - General
Topic: How to Read Pixel Data when Pixel Representation=1
Replies: 6
Views: 5681

Re: How to Read Pixel Data when Pixel Representation=1

Thanks for the reply. However, I still think something is wrong in my code. I picked another image from the pydicom-data repository (emri_small_jpeg_ls_lossless.dcm) which has the following properties. (0002, 0010) Transfer Syntax UID UI: JPEG-LS Lossless Image Compression (0002, 0012) Implementatio...
by samee
Tue, 2023-04-04, 19:06
Forum: DCMTK - General
Topic: How to Read Pixel Data when Pixel Representation=1
Replies: 6
Views: 5681

Re: How to Read Pixel Data when Pixel Representation=1

Yes, the image is compressed with JPEG200. Here is the tag value.

Code: Select all

(0002, 0010) Transfer Syntax UID                 UI: JPEG 2000 Image Compression (Lossless Only)
Is there a way to find the list of the supported compressions for open source DCMTK?

Thanks,
by samee
Tue, 2023-04-04, 17:59
Forum: DCMTK - General
Topic: How to Read Pixel Data when Pixel Representation=1
Replies: 6
Views: 5681

How to Read Pixel Data when Pixel Representation=1

Hello there. I am trying to use the DCMTK API to read some dicom files. The following piece of code works when the Pixel Representation value is 0 (uncompressed image, as I understand). However, when I am trying to read an image with pixel representation value 1, I get an error: Pixel representation...
by samee
Fri, 2023-03-31, 23:16
Forum: DCMTK - General
Topic: Issue with Reading Pixel Data using getUncompressedFrame
Replies: 1
Views: 2969

Issue with Reading Pixel Data using getUncompressedFrame

Hi there, I am trying to read pixel data of a frame directly to an array. I looked at some example code from diinpxt.h file but not sure where I am making the mistake. I have the following code: auto dcm_ff = DcmFileFormat(); auto dcm_tag_pixel_data = DcmTagKey(0x7fe0,0x0010) ; dcm_ff.loadFile("...