MHub Implementation of PyRadiomics #76
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- Include metadata as string in the MHub Metadata column in the generated pyradiomics.csv file. - Make file alignment configurable and deactivated by default (z_align_seg_and_image flag). - Make the parameter file path configurable (config_file).
…17 model" This reverts commit 6d98b78.
This reverts commit a11c010.
…17 model" This reverts commit 6d98b78.
~ model inputs
|
/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.zipTest Results (24.04.18_22.19.05_B87cUA63li)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 |
|
Test passed, model can be merged. |
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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: