Need to update for latest pydicom

[pieper]

Opening a SEG file from IDC LNQ2023 collection I was prompted to install highdicom and then got this error. The SEG loads correctly, but probably SRs would not.

Switch to module:  "DICOM"
Collecting highdicom<=0.22.0
  Downloading highdicom-0.22.0-py3-none-any.whl.metadata (3.8 kB)
Requirement already satisfied: pydicom!=2.4.0,>=2.3.0 in ./Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages (from highdicom<=0.22.0) (3.0.1)
Requirement already satisfied: numpy>=1.19 in ./Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages (from highdicom<=0.22.0) (1.26.4)
Requirement already satisfied: pillow>=8.3 in ./Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages (from highdicom<=0.22.0) (11.2.1)
Collecting pillow-jpls>=1.0 (from highdicom<=0.22.0)
  Downloading pillow_jpls-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB)
Downloading highdicom-0.22.0-py3-none-any.whl (825 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━Downloading pillow_jpls-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (305 kB)
Installing collected packages: pillow-jpls, highdicom

Successfully installed highdicom-0.22.0 pillow-jpls-1.3.2
Traceback (most recent call last):
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/slicer.org/Extensions-34248/QuantitativeReporting/lib/Slicer-5.11/qt-scripted-modules/DICOMTID1500Plugin.py", line 107, in isDICOMTID1500
    import highdicom as hd
ModuleNotFoundError: No module named 'highdicom'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Slicer-5.11/qt-scripted-modules/DICOMLib/DICOMUtils.py", line 827, in getLoadablesFromFileLists
    loadablesByPlugin[plugin] = plugin.examineForImport(fileLists)
                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/slicer.org/Extensions-34248/QuantitativeReporting/lib/Slicer-5.11/qt-scripted-modules/base/DICOMPluginBase.py", line 53, in examineForImport
    loadablesForFiles = self.examineFiles(files)
                        ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/slicer.org/Extensions-34248/QuantitativeReporting/lib/Slicer-5.11/qt-scripted-modules/DICOMTID1500Plugin.py", line 80, in examineFiles
    isDicomTID1500 = self.isDICOMTID1500(dataset)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/slicer.org/Extensions-34248/QuantitativeReporting/lib/Slicer-5.11/qt-scripted-modules/DICOMTID1500Plugin.py", line 111, in isDICOMTID1500
    import highdicom as hd
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages/highdicom/__init__.py", line 1, in <module>
    from highdicom import ann
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages/highdicom/ann/__init__.py", line 2, in <module>
    from highdicom.ann.content import Measurements, AnnotationGroup
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages/highdicom/ann/content.py", line 14, in <module>
    from highdicom.content import AlgorithmIdentificationSequence
  File "/home/exouser/Downloads/Slicer-5.11.0-2025-11-10-linux-amd64/lib/Python/lib/python3.12/site-packages/highdicom/content.py", line 13, in <module>
    from pydicom._storage_sopclass_uids import SegmentationStorage
ModuleNotFoundError: No module named 'pydicom._storage_sopclass_uids'

[pieper]

Note that because of this error, it tries to reinstall highdicom every time you try to load data.

[fedorov]

Who would think python would be more pain to deal with than C++?

It appears that it fails with pydicom 3.0.1. We had to use an older version of highdicom to work around old pydicom in Slicer (see Slicer/Slicer#8796 and #293 (comment)), but I guess we never tested whether old version of highdicom works with the latest version of pydicom. I guess not surprisingly it does not.

Do you have any ideas Steve about how to gracefully handle this kind of an error without regressions to the components that do not require highdicom? Also, did you install pydicom 3.0.1 yourself, or do we have it now in current Slicer?

@deepakri201

[fedorov]

Given Slicer/Slicer#8844, I think the practical way forward is the following:

1. Downgrade QuantitativeReporting in SlicerExtensionIndex to the version that does not have highdicom dependency.
2. Update QuantitativeReporting to use latest highdicom release, assuming pydicom 3.0.1 is available.
3. Once the PR above is merged, update QR version in Slicer to the latest.

[pieper]

I don't have any good suggestion other than adding a version check at runtime to see what's available in the current environment. Now that we have a new stable version I expect the nightly will be changing rapidly (Qt6, etc), so finding a working formula for 5.10, even if it's a bit of a hack, would be a good plan.