soorena62
80 lines
2.4 KiB
Python
80 lines
2.4 KiB
Python
import os
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import pysera
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from app.engine import radiuma_assets
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from app.engine.dagster_builder import radiuma_job
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from dagster import materialize, FilesystemIOManager
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# Main workflow runner for Radiuma using PySERA and Dagster
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def run_workflow():
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# Define input image and mask paths
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image_path = os.path.normpath("data/images/CT_pitch.nii.gz")
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mask_path = os.path.normpath("data/masks/CT_pitch_mask.nii.gz")
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output_dir = os.path.normpath("./results")
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# Run PySERA radiomics workflow
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# Changed dimensions from "3d" to "1st,2D"
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result = pysera.process_batch(
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image_input=image_path,
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mask_input=mask_path,
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output_path=output_dir,
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categories="all",
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dimensions="1st,2D", # <-- only change applied here
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apply_preprocessing=True,
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)
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print("✅ PySERA workflow finished." if result.get("success") else "❌ PySERA workflow failed.")
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def run_pipeline():
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# Run Dagster job with sample configuration
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result = radiuma_job.execute_in_process(
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run_config={
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"ops": {
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"load_image": {"inputs": {"filename": {"value": "CT_pitch.nii.gz"}}},
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"load_mask": {"inputs": {"filename": {"value": "CT_pitch_mask.nii.gz"}}},
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}
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}
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)
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print("✅ Dagster job finished.")
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print(result)
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def run_assets():
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# Ensure artifacts directory exists
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base_dir = os.path.normpath("app/storage/artifacts")
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os.makedirs(base_dir, exist_ok=True)
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# Use FilesystemIOManager for asset storage
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io_manager = FilesystemIOManager(base_dir=base_dir)
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# Materialize all assets defined in radiuma_assets
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result = materialize(
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[
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radiuma_assets.raw_image,
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radiuma_assets.raw_mask,
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radiuma_assets.registered_image,
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radiuma_assets.fused_image,
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radiuma_assets.features,
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],
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resources={"io_manager": io_manager},
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)
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if result.success:
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print("✅ Assets materialized successfully.")
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print(f"Storage base_dir: {base_dir}")
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# Print all materialized asset keys
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for event in result.get_asset_materialization_events():
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print(f"Asset built: {event.asset_key}")
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else:
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print("❌ Asset execution failed.")
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print(result)
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if __name__ == "__main__":
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print("🚀 Starting Radiuma unified run...\n")
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run_workflow()
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run_pipeline()
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run_assets()
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print("\n🎯 All workflows completed in one run.")
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