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MHubAI / models

Stores the MHub models dockerfiles and scripts.
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MHub Implementation of PyRadiomics #76

Closed LennyN95 closed 6 months ago

LennyN95 commented 6 months ago

Implementing the PyRadiomics module into MHub.

PyRadiomics Git Repository: https://github.com/AIM-Harvard/pyradiomics PyRadiomics Docs: https://pyradiomics.readthedocs.io/en/latest/

This MHub implementation provides a pipeline starting from DICOM image data and DICOM segmentation data (DICOMSEG) for radiomic feature extraction with the pyradiomics Python package.

Test-Data from IDC:
Collection TCGA-LIHC
Case TCGA-BC-A10Z
Study 1.3.6.1.4.1.14519.5.2.1.8421.4008.338750756821159002165351451130
Image (CT, Arterial Phase) 1.3.6.1.4.1.14519.5.2.1.8421.4008.761093011533106086639756339870
Image (AWS Link) s3://idc-open-data/86a34cf5-cfdb-4cc5-98df-b5167706b5d3/*
Segmentation (Liver) 1.2.276.0.7230010.3.1.3.17436516.270878.1696966588.943239
Segmentation (AWS Link) s3://idc-open-data/1bbc9a0e-b5c2-4d56-a108-97623d44a703/*
LennyN95 commented 6 months ago

/test

sample:
  idc_version: "Data Release 17.0 December 04, 2023"
  data:
  - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.8421.4008.761093011533106086639756339870
    aws_url: s3://idc-open-data/86a34cf5-cfdb-4cc5-98df-b5167706b5d3/*
    path: dicom
  - SeriesInstanceUID: 1.2.276.0.7230010.3.1.3.17436516.270878.1696966588.943239
    aws_url: s3://idc-open-data/1bbc9a0e-b5c2-4d56-a108-97623d44a703/*
    path: dicom

reference:
  url: https://github.com/MHubAI/models/files/15030158/pyradiomics_test_output.zip
Test Results (24.04.18_22.19.05_B87cUA63li) ```yaml id: 50098d28-4eec-47e3-be7c-09c00b38c829 date: '2024-04-18 22:22:32' checked_files: - file: pyradiomics.csv path: /app/test/src/1.3.6.1.4.1.14519.5.2.1.8421.4008.761093011533106086639756339870/pyradiomics.csv checks: - checker: DataFileCheck notes: - label: Value Match description: These keys have identical values info: '[0].Image,[0].Mask,[0].Label,[0].Label_channel,[0].MHub ROI,[0].MHub Metadata,[0].diagnostics_Versions_PyRadiomics,[0].diagnostics_Versions_Numpy,[0].diagnostics_Versions_SimpleITK,[0].diagnostics_Versions_PyWavelet,[0].diagnostics_Versions_Python,[0].diagnostics_Configuration_Settings,[0].diagnostics_Configuration_EnabledImageTypes,[0].diagnostics_Image-original_Hash,[0].diagnostics_Image-original_Dimensionality,[0].diagnostics_Image-original_Spacing,[0].diagnostics_Image-original_Size,[0].diagnostics_Image-original_Mean,[0].diagnostics_Image-original_Minimum,[0].diagnostics_Image-original_Maximum (+ 108 more)' - checker: SizeCheck summary: files_missing: 0 files_extra: 0 checks: DataFileCheck: files: 1 SizeCheck: files: 1 conclusion: true ```
LennyN95 commented 6 months ago

Test passed, model can be merged.