soorena62
74 lines
2.6 KiB
Python
74 lines
2.6 KiB
Python
# ops_reader.py
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from dagster import op
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import os
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import pysera
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@op
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def read_images():
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# Match Radiuma.exe by processing a single pair or a flat folder.
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# Here we keep folders; PySERA will find matching pairs.
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image_dir = "data/images"
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mask_dir = "data/masks"
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return {"image_dir": image_dir, "mask_dir": mask_dir}
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@op
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def extract_features(data):
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# Exact PySERA config mirrored from Radiuma.exe logs
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result = pysera.process_batch(
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image_input=data["image_dir"],
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mask_input=data["mask_dir"],
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output_path="./artifacts/results",
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# Core run behavior
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enable_parallelism=False,
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num_workers=1,
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apply_preprocessing=True,
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roi_selection_mode="per_region",
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roi_num=2,
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min_roi_volume=50,
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feature_value_mode="REAL_VALUE",
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# Feature scope
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categories="diag,morph,glcm,glrlm,glszm,ngtdm,ngldm",
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dimensions="1st,2D",
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bin_size=25,
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# Logging/report
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report="info",
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# Temp path (matching Radiuma.exe run)
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temporary_files_path=r"C:\Users\Omen16\AppData\Local\ViSERA\res\memory\memmap\pysera_temp",
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# IBSI-based parameters mirrored from Radiuma.exe
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IBSI_based_parameters={
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"radiomics_DataType": "CT",
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"radiomics_DiscType": "FBS",
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"radiomics_isScale": 0,
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"radiomics_VoxInterp": "Nearest",
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"radiomics_ROIInterp": "Nearest",
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"radiomics_isotVoxSize": 1.0,
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"radiomics_isotVoxSize2D": 2.0,
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"radiomics_isIsot2D": 0,
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"radiomics_isGLround": 0,
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"radiomics_isReSegRng": 0,
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"radiomics_isOutliers": 0,
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"radiomics_isQuntzStat": 1,
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"radiomics_ReSegIntrvl01": -1000,
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"radiomics_ReSegIntrvl02": 400,
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"radiomics_ROI_PV": 0.5,
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"radiomics_qntz": "Uniform",
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"radiomics_IVH_Type": 3,
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"radiomics_IVH_DiscCont": 1,
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"radiomics_IVH_binSize": 2.0,
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},
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)
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return result
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@op
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def write_report(result):
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os.makedirs("artifacts", exist_ok=True)
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report_path = "artifacts/radiomics_batch_report_radiuma_match.txt"
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with open(report_path, "w") as f:
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f.write(f"Success: {result['success']}\n")
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f.write(f"Processed files: {result['processed_files']}\n")
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f.write(f"Processing time: {result['processing_time']:.2f} seconds\n")
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f.write(f"Output path: {result['output_path']}\n")
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f.write("Note: Excel with Radiomics_Features, Parameters, Report is saved in output_path.\n")
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return report_path |