fix: more errors due to smaps.

Author: paquiteau

src/snake/core/engine/nufft.py

@@ -28,7 +28,7 @@ def _job_trajectories(
         dataset: mrd.Dataset,
         hdr: mrd.xsd.ismrmrdHeader,
         sim_conf: SimConfig,
-        shot_idx: Sequence[int],
+        shot_idx: Sequence[int] | int,
     ) -> NDArray:
         """Get Non Cartesian trajectories from the dataset.
 
@@ -72,10 +72,12 @@ def _init_model_nufft(
         if slice_2d:
             shape_ = sim_conf.shape[:-1]
             if smaps is not None:
-                smaps_ = smaps[..., 0]
+                smaps_ = np.ascontiguousarray(
+                    smaps[..., 0]
+                )  # will be updated in the loop
 
         nufft = get_operator(backend)(
-            samples,  # dummy samples locs
+            samples,  # will be updated in the loop
             shape=shape_,
             n_coils=n_coils,
             smaps=smaps_,
@@ -121,7 +123,7 @@ def _job_model_T2s(
                 slice_loc = round((traj[0, -1] + 0.5) * sim_conf.shape[-1])
                 nufft.samples = traj[:, :2]
                 if phantom.smaps is not None:
-                    nufft.smaps = phantom.smaps[..., slice_loc]
+                    nufft.smaps = np.ascontiguousarray(phantom.smaps[..., slice_loc])
                 phantom_state = phantom_state[:, None, ..., slice_loc]
             else:
                 phantom_state = phantom_state[:, None, ...]

src/snake/core/phantom/static.py

@@ -66,7 +66,9 @@ def add_tissue(
         masks = np.concatenate((self.masks, mask[None, ...]), axis=0)
         labels = np.concatenate((self.labels, np.array([tissue_name])))
         props = np.concatenate((self.props, props), axis=0)
-        return Phantom(phantom_name or self.name, masks, labels, props)
+        return Phantom(
+            phantom_name or self.name, masks, labels, props, smaps=self.smaps
+        )
 
     @property
     def labels_idx(self) -> dict[str, int]: