511 - anonymisation for spectroscopy data

mxochicale commented 1 month ago

Description

Fixes #511 Adds config files for mr-spectroscopy, including tags RF Echo Train Length Attribute and MR Timing and Related Parameters Sequence Attribute that James Moggridge mentioned is fine to keep them.

Type of change

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[x] New feature (non-breaking change which adds functionality)

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codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 87.15%. Comparing base (80f5dcf) to head (29b3136).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #513 +/- ## ======================================= Coverage 87.15% 87.15% ======================================= Files 76 76 Lines 3464 3464 ======================================= Hits 3019 3019 Misses 445 445 ```

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mxochicale commented 3 weeks ago

Just added https://github.com/SAFEHR-data/PIXL/pull/513/commits/dff1b18a84267c2921786b3806394e4c196a36d3 with some ~20% of unformatted tags from dicom.dcmread(DICOM/csi_slaser_40_20_MR/1.dcm Do we need to include all tags of 1.dcm in the config format mr-spectroscopy.yaml? Maybe yes?, so you can then do more pre-processing and selection to where those tags belong to?

p-j-smith commented 2 weeks ago

if you wanted to test this you create a temporary config using pixldefaulttag.yaml or whatever the placeholder value is when we add the pixl project tag to the instance on reciept. THen could upload some spectroscopy files manually into orthanc raw and that'll move it along to orthanc anon for anonymisation

ah that's a good idea, thanks!

SAFEHR-data / PIXL