fix: more smaps updates required.

Author: paquiteau

src/snake/core/handlers/activations/activations.py

@@ -113,6 +113,7 @@ def get_static(self, phantom: Phantom, sim_config: SimConfig) -> Phantom:
             props=np.concatenate(
                 (phantom.props, phantom.props[tissue_index, :]),
                 axis=0,
+                smaps=phantom.smaps,
             ),
         )
         new_phantom = phantom.add_tissue(

src/snake/core/phantom/static.py

@@ -73,15 +73,21 @@ def labels_idx(self) -> dict[str, int]:
         """Get the index of the labels."""
         return {label: i for i, label in enumerate(self.labels)}
 
-    def get_smaps(
+    def make_smaps(
         self, n_coils: int = None, sim_conf: SimConfig = None, antenna: str = "birdcage"
     ) -> None:
         """Get coil sensitivity maps for the phantom."""
         if n_coils is None and sim_conf is not None:
             n_coils = sim_conf.hardware.n_coils
-
-        if n_coils > 1 and self.smaps is None:
+        elif sim_conf is None and n_coils is None:
+            raise ValueError("Either n_coils or sim_conf must be provided.")
+        if n_coils == 1:
+            log.warning("Only one coil, no need for smaps.")
+        elif n_coils > 1 and self.smaps is None:
             self.smaps = get_smaps(self.anat_shape, n_coils=n_coils, antenna=antenna)
+            log.debug(f"Created smaps for {n_coils} coils.")
+        elif self.smaps is not None:
+            log.warning("Smaps already exists.")
 
     @classmethod
     def from_brainweb(

src/snake/mrd_utils/loader.py

@@ -98,7 +98,9 @@ def iter_frames(
             for i in np.arange(start, stop, step):
                 yield i, *self.get_kspace_frame(i)
 
-    def get_kspace_frame(self, idx: int) -> tuple[NDArray[np.float32], NDArray[np.complex64]]:
+    def get_kspace_frame(
+        self, idx: int
+    ) -> tuple[NDArray[np.float32], NDArray[np.complex64]]:
         """Get k-space frame trajectory/mask and data."""
         raise NotImplementedError()
 
@@ -233,16 +235,15 @@ def get_phantom(self, imnum: int = 0) -> Phantom:
         name = image.meta.pop("name")
         labels = np.array(image.meta["labels"].split(","))
         props = unserialize_array(image.meta["props"])
-
+        smaps = self.get_smaps()
         return Phantom(
             masks=image.data,
             labels=labels,
             props=props,
             name=name,
+            smaps=smaps,
         )
 
-        return Phantom.from_mrd_dataset(self)
-
     @cached_property
     def _all_waveform_infos(self) -> dict[int, dict]:
         return parse_waveform_information(self.header)