Integration of Python packages meeting?

[matthew-brett]

By @ matthew.brett on July 27, 2021, 5:23pm

This follows on from a discussion in the last meeting - is it now time to have a meeting to think about how to divide up the work and code between dicom_parser, Nibabel and dcmstack?

Zvi - would it be imposing to ask you to organize again? I'm also happy to do it...

[matthew-brett]

By @ baratzz on July 30, 2021, 2:11pm

@ matthew.brett
Sorry I missed this thread - no problem. I have a pretty busy weekend, but I'll send a Doodle link in a couple of days.

[matthew-brett]

By @ baratzz on August 4, 2021, 8:48am

@ matthew.brett @ effigies
Let's meet tomorrow at 11:00 AM Pacific time.
Please use this link to join.

[matthew-brett]

By @ effigies on August 4, 2021, 1:58pm

Hi @ baratzz. I completely spaced and have competing obligations tomorrow. If push comes to shove, I can make it, but are there any other days that work?

[matthew-brett]

By @ baratzz on August 4, 2021, 2:05pm

No problem, Friday at 12 PM?

[matthew-brett]

By @ effigies on August 4, 2021, 2:16pm

Yes, I can make 12pm PDT on Friday.

[matthew-brett]

By @ effigies on August 6, 2021, 8:30pm

Notes:

• Coordinating DICOM data repository (forking from @ neurolabusc?)
• Convert Li et al to issues on dicom_parser repository
• (De)serializing to/from NIfTI
• xprotocol parsing - GitHub -matthew-brett/xprotp; WIP: Improve meta data extraction from DICOM files by moloney · Pull Request #290 · nipy/nibabel ·GitHub

Rough order of package dependency:

• nixbabel
  • nibabel
    • dicom_parser
      • pydicom
      • numpy
      • [xarray]
  • xarray

[matthew-brett]

By @ matthew.brett on August 6, 2021, 8:57pm

Just adding from discussion - some tasks:

Working out how to serialize an xarray image to Nifti with a JSON header extension, and then load it back again. XArray has its own JSON format (just expanding on Chris' point there).

Review Brendan's dcmstack PR for Nibabel, and particularly : nipy/nibabel#1030

Discuss moving xprotocol parsing to dicom_parser.