511 - anonymisation for spectroscopy data

[mxochicale]

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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• New feature (non-breaking change which adds functionality)

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 87.35%. Comparing base (83cc35a) to head (e8835ab).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #513   +/-   ##
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  Coverage   87.35%   87.35%           
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  Files          76       76           
  Lines        3378     3378           
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  Hits         2951     2951           
  Misses        427      427           

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[stefpiatek]

Just want to check that you've gone through all the tags that are in both spectroscopy example studies? Surprising that there's only two extra tags on top of MRI at least at first glance

[mxochicale]

Just added dff1b18 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]

I've updated the mr-spectroscopy config file with tags that cause the validation to fail, and I've not yet included all nested tags except for those that are required by the validator

[stefpiatek]

let me know when you want a review but adding in a quick comment

[stefpiatek]

Thanks for getting this in, if you wanted to test this you create a temporary config using pixl__default__tag.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

[p-j-smith]

if you wanted to test this you create a temporary config using pixl__default__tag.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!