Add All Folders

2026-02-08 04:38:10 +03:30
commit 9bb57e4799
191 changed files with 8469 additions and 0 deletions
@@ -0,0 +1,74 @@
+# ops_reader.py
+from dagster import op
+import os
+import pysera
+
+@op
+def read_images():
+    # Match Radiuma.exe by processing a single pair or a flat folder.
+    # Here we keep folders; PySERA will find matching pairs.
+    image_dir = "data/images"
+    mask_dir = "data/masks"
+    return {"image_dir": image_dir, "mask_dir": mask_dir}
+
+@op
+def extract_features(data):
+    # Exact PySERA config mirrored from Radiuma.exe logs
+    result = pysera.process_batch(
+        image_input=data["image_dir"],
+        mask_input=data["mask_dir"],
+        output_path="./artifacts/results",
+        # Core run behavior
+        enable_parallelism=False,
+        num_workers=1,
+        apply_preprocessing=True,
+        roi_selection_mode="per_region",
+        roi_num=2,
+        min_roi_volume=50,
+        feature_value_mode="REAL_VALUE",
+        # Feature scope
+        categories="diag,morph,glcm,glrlm,glszm,ngtdm,ngldm",
+        dimensions="1st,2D",
+        bin_size=25,
+        # Logging/report
+        report="info",
+        # Temp path (matching Radiuma.exe run)
+        temporary_files_path=r"C:\Users\Omen16\AppData\Local\ViSERA\res\memory\memmap\pysera_temp",
+        # IBSI-based parameters mirrored from Radiuma.exe
+        IBSI_based_parameters={
+            "radiomics_DataType": "CT",
+            "radiomics_DiscType": "FBS",
+            "radiomics_isScale": 0,
+            "radiomics_VoxInterp": "Nearest",
+            "radiomics_ROIInterp": "Nearest",
+            "radiomics_isotVoxSize": 1.0,
+            "radiomics_isotVoxSize2D": 2.0,
+            "radiomics_isIsot2D": 0,
+            "radiomics_isGLround": 0,
+            "radiomics_isReSegRng": 0,
+            "radiomics_isOutliers": 0,
+            "radiomics_isQuntzStat": 1,
+            "radiomics_ReSegIntrvl01": -1000,
+            "radiomics_ReSegIntrvl02": 400,
+            "radiomics_ROI_PV": 0.5,
+            "radiomics_qntz": "Uniform",
+            "radiomics_IVH_Type": 3,
+            "radiomics_IVH_DiscCont": 1,
+            "radiomics_IVH_binSize": 2.0,
+        },
+    )
+    return result
+
+@op
+def write_report(result):
+    os.makedirs("artifacts", exist_ok=True)
+    report_path = "artifacts/radiomics_batch_report_radiuma_match.txt"
+
+    with open(report_path, "w") as f:
+        f.write(f"Success: {result['success']}\n")
+        f.write(f"Processed files: {result['processed_files']}\n")
+        f.write(f"Processing time: {result['processing_time']:.2f} seconds\n")
+        f.write(f"Output path: {result['output_path']}\n")
+        f.write("Note: Excel with Radiomics_Features, Parameters, Report is saved in output_path.\n")
+
+    return report_path