dicom-anonymiser Generic Wrapper Microservice

[darshad-github]

Proposed Changes

This pull request is initiated to review development progress against gitlab issue #137 which is to design a C# generic wrapper microservice that can call external scripts to anonymise DICOM files.

Proposed Changes (06-02-2024):

As a reusable component, this microservice takes a message, performs CTP anonymisation followed by SR anonymisation or DICOM anonymisation on the dicom file based on the image modality. It creates a new anonymised file, and finally generates a message containing the new filename. Additionally, the microservice is able to handle the failure of the script.

• Branch: feature/dicom-anonymiser
  • Renamed existing class DicomAnonymiser to DefaultAnonymiser that implements the IDicomAnonymiser interface responsible for anonymising DICOM files.
  • Modified the Anonymise method across 3 different anonymisation methods (CreateCTPProcess, CreateDICOMProcess, CreateSRProcess) which creates the required process based on different configs.
  • Add a new method called CreateDICOMToTextProcess responsible for converting dicom files to text required by CreateSRProcess.
  • Modified the configuration file, DicomAnonymiserConfigs.json with additional paths required for setting up CTP and SR anonymisation process.
  • Modified the DicomAnonymiserConsumer class to include a DicomFile object using the FellowOakDicom package to extract message modality.
  • Updated the GlobalOptions.cs class with the required dicom anonymiser configurations and removed DicomAnonymiserConfigs.json altogether.

Proposed Changes (22-11-2023):

As a reusable component, this microservice takes a message, performs pixel data anonymisation on the dicom file, creates a new anonymised file, and finally generates a message containing the new filename. Additionally, the microservice is able to handle the failure of the script.

• Branch: feature/dicom-anonymiser
  • Introduced a new class DicomAnonymiser that implements the IDicomAnonymiser interface responsible for anonymising DICOM files.
  • Modified the Anonymise method in the IDicomAnonymiser interface to include an additional ExtractFileMessage parameter.
  • Added the DicomAnonymiser value to the AnonymiserType enum to represent the DICOM file anonymiser.
  • Updated the AnonymiserFactory to create a new instance of DicomAnonymiser when the DicomAnonymiser type is specified.
  • Added a new configuration file, DicomAnonymiserConfigs.json which contains paths setting up the anonymisation process.
  • Updated the DicomAnonymiserConsumer class to use the DicomAnonymiser for anonymising files.

Service Documentation:

• A confluence page has been created to document a quick start guide for the new service and will be pushed in the repository once the development has been completed.
  DRAFT-Dicom-Anonymiser Generic Wrapper Microservice-221123

Types of changes

What types of changes does your code introduce? Tick all that apply.

• Bugfix (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)
• Documentation-Only Update (if none of the other choices apply)
  • In this case, ensure that the message of the head commit from the source branch is prefixed with [skip ci]

Checklist

By opening this PR, I confirm that I have:

• Reviewed the contributing guidelines for this repository
• Ensured that the PR branch is in sync with the target branch (i.e. it is automatically merge-able)
• Updated any relevant API documentation
• Created or updated any tests if relevant
• Created a news file
  • NOTE: This must include any changes to any of the following files: default.yaml, any of the RabbitMQ server configurations, GlobalOptions.cs
• Listed myself in the CONTRIBUTORS file 🚀
• Requested a review by one of the repository maintainers

Issues

If relevant, tag any issues that are expected to be resolved with this PR. E.g.:

• Linked GitLab Issue #137
• ...

[rkm]

Still a little early in development for a full review, but I've left one comment in the meantime. Happy to discuss working in the GlobalOptions class and working through some of the TODOs!

[codecov]

Codecov Report

Attention: Patch coverage is 23.80952% with 64 lines in your changes missing coverage. Please review.

Project coverage is 59.19%. Comparing base (c0038ad) to head (392eee2).

Files	Patch %	Lines
...s.DicomAnonymiser/Anonymisers/DefaultAnonymiser.cs	0.00%	54 Missing ⚠️
...ervices.DicomAnonymiser/DicomAnonymiserConsumer.cs	61.90%	6 Missing and 2 partials ⚠️
...s.DicomAnonymiser/Anonymisers/AnonymiserFactory.cs	50.00%	1 Missing ⚠️
...croservices.DicomAnonymiser/DicomAnonymiserHost.cs	0.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1679      +/-   ##
==========================================
- Coverage   59.82%   59.19%   -0.63%     
==========================================
  Files         176      177       +1     
  Lines        6312     6391      +79     
  Branches      861      877      +16     
==========================================
+ Hits         3776     3783       +7     
- Misses       2294     2363      +69     
- Partials      242      245       +3     

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