Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add configuration for DESPIAD project #572

Open
wants to merge 52 commits into
base: main
Choose a base branch
from
Open

Conversation

p-j-smith
Copy link
Contributor

@p-j-smith p-j-smith commented Dec 12, 2024

Description

Closes #571
Closes #530

  • add project config for DESPIAD
  • add tag operation files for CT and PET
  • use base, CT, then PET tag operation files for anonymisation
  • ensure all resources sharing a StudyInstanceUID in Orthanc Raw are exported (they may exist as separate resources in Orthanc Raw if they have different StudyIDs, but are combined into a single resource in Orthanc Anon as the StudyID tag is deleted) This has already been fixed in Improve anon logging and anonymise all matching studies at once #582

Type of change

Please delete options accordingly to the description.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

Suggested Checklist

  • I have performed a self-review of my own code.
  • I have made corresponding changes to the documentation.
  • My changes generate no new warnings.
  • I have commented my code, particularly in hard-to-understand areas.
  • I have passed on my local host device. (see further details at the CONTRIBUTING document)
  • Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
  • I have requested review to this PR.
  • I have addressed and marked as resolved all the review comments in my PR.
  • Finally, I have selected squash and merge

this is because resources sharing the same StudyInstanceUID in Orthanc Raw will be combined into a single resource in Orthanc Anon.
Previously, we would try to export each resource after anonymisation, but this meant other resources sharing the same StudyInstanceUID were not exported.
Copy link

codecov bot commented Dec 12, 2024

Codecov Report

Attention: Patch coverage is 93.40659% with 6 lines in your changes missing coverage. Please review.

Project coverage is 85.50%. Comparing base (4af6ed0) to head (ecb04ce).

Files with missing lines Patch % Lines
pixl_dcmd/src/pixl_dcmd/main.py 88.88% 4 Missing ⚠️
..._core/src/core/project_config/pixl_config_model.py 92.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #572      +/-   ##
==========================================
- Coverage   87.51%   85.50%   -2.02%     
==========================================
  Files          76       72       -4     
  Lines        3437     3235     -202     
==========================================
- Hits         3008     2766     -242     
- Misses        429      469      +40     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@p-j-smith p-j-smith marked this pull request as ready for review January 15, 2025 10:34
Copy link
Contributor Author

@p-j-smith p-j-smith left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

do we know the allowed_manufactures we should add for each project?

pixl_dcmd/tests/test_main.py Outdated Show resolved Hide resolved
Copy link
Contributor

@stefpiatek stefpiatek left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looking good, but I think we need to be careful about despiad series to filter out. At least checking an example from each manufacturer for each modality to ensure that we're not exporting burned in PID

projects/configs/despiad.yaml Outdated Show resolved Hide resolved
projects/configs/despiad.yaml Outdated Show resolved Hide resolved
template_config.yaml Outdated Show resolved Hide resolved
template_config.yaml Outdated Show resolved Hide resolved
template_config.yaml Outdated Show resolved Hide resolved
Copy link
Contributor Author

@p-j-smith p-j-smith left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think it's nearly ready to merge, just a couple of questions about what defaults we want

README.md Outdated Show resolved Hide resolved
Comment on lines +15 to +30
- name: Series Date
group: 0x0008
element: 0x0021
op: replace
- name: Acquisition Date
group: 0x0008
element: 0x0022
op: replace
- name: Series Time
group: 0x0008
element: 0x0031
op: keep
- name: Acquisition Time
group: 0x0008
element: 0x0032
op: keep
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should we be replacing the times by default? Dave suggested we default to keeping them:

More information about the acquisition (reconstrution, randoms correction, etc) is also useful to ensure study protocol compliance in single and multi-centre studies. Acquisition time is a Level 1 attribute for PET series. And I think it may be worth keeping time to ensure uptake time, especially as in the PET base module all of the dates are either replace or wiped out.

Copy link
Contributor

@stefpiatek stefpiatek Feb 4, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think we're probably okay but worth dropping Sophie an email to get her take on it from an IG perspective

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Add config for DESPIAD PIXL pipeline for CT data
3 participants