Add All Folders

2026-02-08 04:38:10 +03:30
commit 9bb57e4799
191 changed files with 8469 additions and 0 deletions
@@ -0,0 +1,79 @@
+import os
+import pysera
+from app.engine import radiuma_assets
+from app.engine.dagster_builder import radiuma_job
+from dagster import materialize, FilesystemIOManager
+
+# Main workflow runner for Radiuma using PySERA and Dagster
+
+def run_workflow():
+    # Define input image and mask paths
+    image_path = os.path.normpath("data/images/CT_pitch.nii.gz")
+    mask_path  = os.path.normpath("data/masks/CT_pitch_mask.nii.gz")
+    output_dir = os.path.normpath("./results")
+
+    # Run PySERA radiomics workflow
+    # Changed dimensions from "3d" to "1st,2D"
+    result = pysera.process_batch(
+        image_input=image_path,
+        mask_input=mask_path,
+        output_path=output_dir,
+        categories="all",
+        dimensions="1st,2D",  # <-- only change applied here
+        apply_preprocessing=True,
+    )
+    print("✅ PySERA workflow finished." if result.get("success") else "❌ PySERA workflow failed.")
+
+
+def run_pipeline():
+    # Run Dagster job with sample configuration
+    result = radiuma_job.execute_in_process(
+        run_config={
+            "ops": {
+                "load_image": {"inputs": {"filename": {"value": "CT_pitch.nii.gz"}}},
+                "load_mask":  {"inputs": {"filename": {"value": "CT_pitch_mask.nii.gz"}}},
+            }
+        }
+    )
+    print("✅ Dagster job finished.")
+    print(result)
+
+
+def run_assets():
+    # Ensure artifacts directory exists
+    base_dir = os.path.normpath("app/storage/artifacts")
+    os.makedirs(base_dir, exist_ok=True)
+
+    # Use FilesystemIOManager for asset storage
+    io_manager = FilesystemIOManager(base_dir=base_dir)
+
+    # Materialize all assets defined in radiuma_assets
+    result = materialize(
+        [
+            radiuma_assets.raw_image,
+            radiuma_assets.raw_mask,
+            radiuma_assets.registered_image,
+            radiuma_assets.fused_image,
+            radiuma_assets.features,
+        ],
+        resources={"io_manager": io_manager},
+    )
+
+    if result.success:
+        print("✅ Assets materialized successfully.")
+        print(f"Storage base_dir: {base_dir}")
+
+        # Print all materialized asset keys
+        for event in result.get_asset_materialization_events():
+            print(f"Asset built: {event.asset_key}")
+    else:
+        print("❌ Asset execution failed.")
+        print(result)
+
+
+if __name__ == "__main__":
+    print("🚀 Starting Radiuma unified run...\n")
+    run_workflow()
+    run_pipeline()
+    run_assets()
+    print("\n🎯 All workflows completed in one run.")