MHub / GC - Add the GC stoic baseline model

[silvandeleemput]

This PR adds the GC STOIC baseline model (from the STOIC2021 challenge) to MHub.
GitHub Repo: https://github.com/luukboulogne/stoic2021-baseline
GC page: https://grand-challenge.org/algorithms/stoic2021-baseline/

Algorithm I/O

• Input should be a CT Lung image (MHA) (This MHub implementation expects a Dicom which is converted to MHA using MhaConverter)
• Outputs are:
  • A JSON file with the following output scores:
    *probability-covid-19
    *probability-severe-covid-19
• Test images for this algorithm can be downloaded from here: https://stoic2021.grand-challenge.org/stoic-db/

Caveats

• The PR target is main, but should be something like m-gc-stoic-baseline
• In the Dockerfile the MHub model repo integration is currently marked TODO since it requires the creation of the appropriate branch for this code first.
• Added a TODO to the MHAConverter since it doesn't have the panimg backend yet.

[LennyN95]

I suggest we use ValueOutput in combination with a ReportExporter.

[silvandeleemput]

I suggest we use ValueOutput in combination with a ReportExporter.

I'll add these soon.

[silvandeleemput]

The ValueOutputs and ReportExporter have been added, plus some minor cleanup.

[silvandeleemput]

The repository commit has been fixed and additional comments have been added to the runner.

[silvandeleemput]

I removed the ValueOutput.Meta lines and updated the Dockerfile with the new import

[silvandeleemput]

output.zip

[silvandeleemput]

/test

sample:
  idc_version: 17.0
  data:
    - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357
      aws_url: s3://idc-open-data/6079cc3b-4b0f-41ec-bdbb-c6e754e88229/*
      path: dicom

reference:
  url: https://github.com/MHubAI/models/files/14650741/output.zip

---

Test Results (24.03.28_17.30.31_kb1YE6N1mX)

id: c50ad4de-ce35-4a60-a22e-85029c1ed031
date: '2024-03-28 18:03:49'
checked_files:
- file: gc_stoic_baseline_covid_scores.json
  path: /app/test/src/1.3.6.1.4.1.14519.5.2.1.6279.6001.141365756818074696859567662357/gc_stoic_baseline_covid_scores.json
  checks:
  - checker: DataFileCheck
    findings:
    - label: Value similar
      description: Value of key 'probability-covid-19' is similar in source file
      subpath: probability-covid-19
      info:
        scale: 1
        precision: 5
        src: 0.5520431399345398
        ref: 0.5520455241203308
    - label: Value similar
      description: Value of key 'probability-severe-covid-19' is similar in source
        file
      subpath: probability-severe-covid-19
      info:
        scale: 1
        precision: 4
        src: 0.5822800993919373
        ref: 0.5822792053222656
  - checker: SizeCheck
summary:
  files_missing: 0
  files_extra: 0
  checks:
    DataFileCheck:
      files: 1
      findings:
        Value similar: 2
    SizeCheck:
      files: 1
conclusion: false

[silvandeleemput]

/review

The meta.json file has been updated and the comments have been addressed.