Add All Folders

Luigi/engine/tasks_reader.py

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+import os
+import luigi
+import SimpleITK as sitk
+from pathlib import Path
+from engine.utils import ensure_dir
+
+class ImageReader(luigi.Task):
+    data_dir = luigi.Parameter(default=os.path.join("data", "images"))
+    artifacts_dir = luigi.Parameter(default="artifacts")
+
+    def output(self):
+        out_dir = ensure_dir(Path(self.artifacts_dir) / "reader")
+        return luigi.LocalTarget(str(out_dir / "reader_index.txt"))
+
+    def run(self):
+        reader_dir = ensure_dir(Path(self.artifacts_dir) / "reader")
+        files = [os.path.join(self.data_dir, f) for f in os.listdir(self.data_dir) if f.endswith(".nii.gz")]
+        if not files:
+            raise FileNotFoundError("No images found in data/images")
+        converted_paths = []
+        for path in files:
+            img = sitk.ReadImage(path)
+            img_float = sitk.Cast(img, sitk.sitkFloat32)
+            out_path = reader_dir / f"reader_{Path(path).name}"
+            sitk.WriteImage(img_float, str(out_path))
+            converted_paths.append(str(out_path))
+        with self.output().open("w") as f:
+            f.write("\n".join(converted_paths))