added v2 baseline

Author: vaibhavbahel

src/baseline/check_dataset_shapes.py src/baseline/v1/check_dataset_shapes.pysrc/baseline/check_dataset_shapes.py renamed to src/baseline/v1/check_dataset_shapes.py

@@ -0,0 +1,73 @@
+import os
+import nibabel as nib
+import numpy as np
+
+DATA_DIR = "/depict/users/hinge/shared/bic-mac-data/hf_dataset/train"
+
+FILES = {
+    "pet": "features/nacpet.nii.gz",
+    "topogram": "features/topogram.nii.gz",
+    "mri_in": "features/mri_combined_in_phase.nii.gz",
+    "mri_out": "features/mri_combined_out_phase.nii.gz",
+    "ct": "ct-label/ct.nii.gz",
+}
+
+
+def load_info(path):
+
+    img = nib.load(path)
+
+    shape = img.shape
+    spacing = img.header.get_zooms()
+
+    affine = img.affine
+    det = np.linalg.det(affine[:3, :3])
+
+    return shape, spacing, det
+
+
+def main():
+
+    subjects = sorted(os.listdir(DATA_DIR))
+
+    print("\nChecking dataset:\n")
+
+    for sub in subjects:
+
+        print("=" * 70)
+        print("Subject:", sub)
+
+        base = os.path.join(DATA_DIR, sub)
+
+        for key, relpath in FILES.items():
+
+            path = os.path.join(base, relpath)
+
+            if not os.path.exists(path):
+                print(f"{key:10s} MISSING")
+                continue
+
+            try:
+
+                shape, spacing, det = load_info(path)
+
+                print(
+                    f"{key:10s} | shape={str(shape):20s} "
+                    f"| spacing={str(spacing):20s} "
+                    f"| det={det:.4f}"
+                )
+
+                if det == 0:
+                    print("  ⚠ WARNING: affine determinant is ZERO")
+
+            except Exception as e:
+
+                print(f"{key:10s} ERROR: {e}")
+
+        print()
+
+    print("\nDone.\n")
+
+
+if __name__ == "__main__":
+    main()

src/baseline/configs/config.yaml src/baseline/v1/configs/config.yamlsrc/baseline/configs/config.yaml renamed to src/baseline/v1/configs/config.yaml

@@ -0,0 +1,17 @@
+data_dir: /depict/users/hinge/shared/bic-mac-data/hf_dataset/train
+
+batch_size: 2
+num_workers: 0
+
+epochs: 250
+learning_rate: 0.0003
+
+patch_size: [192,192,192]
+
+spacing: [2.0,2.0,2.0]
+
+input_modalities:
+  - nacpet
+  - topogram
+  - mri_combined_in_phase
+  - mri_combined_out_phase