fix: wrong rebase

Author: paquiteau

src/mrinufft/io/__init__.py

@@ -9,7 +9,7 @@
 __all__ = [
     "cfl2traj",
     "prepare_trajectory_for_seq",
-    "pulseq_gre_3D",
+    "pulseq_gre",
     "read_arbgrad_rawdat",
     "read_pulseq_traj",
     "read_siemens_rawdat",

src/mrinufft/io/nsp.py

@@ -312,12 +312,15 @@ def write_trajectory(
         if postgrad == "slowdown_to_edge":
             # Always end at KMax, the spoilers can be handeled by the sequence.
             edge_locations[..., 0] = img_size[0] / FOV[0] / 2
-        end_gradients = get_gradient_amplitudes_to_travel_for_set_time(
-            kspace_end_loc=edge_locations,
-            start_gradients=gradients[:, -1],
-            kspace_start_loc=final_positions,
-            acq=acq,
-        )
+            end_gradients = get_gradient_amplitudes_to_travel_for_set_time(
+                kspace_end_loc=edge_locations,
+                start_gradients=gradients[:, -1],
+                kspace_start_loc=final_positions,
+                acq=acq,
+            )
+
+            gradients = np.hstack([gradients, end_gradients])
+            Ns_to_skip_at_end = end_gradients.shape[1]
     # Check constraints if requested
     if check_constraints:
         slewrates, _ = convert_gradients_to_slew_rates(gradients, acq)

src/mrinufft/io/pulseq.py

@@ -109,7 +109,7 @@ def pulseq_gre(
     rf_pulse: SimpleNamespace | None = None,
     rf_spoiling_inc: float = 0.0,
     grad_spoil_factor: float = 2.0,
-    system = None,
+    system=None,
     osf: int = 1,
 ):
     """Create a Pulseq 3D-GRE sequence for arbitrary trajectories.

src/mrinufft/trajectories/tools.py

@@ -644,13 +644,13 @@ def _residual(gi):
     nb_shots, nb_dimension = kspace_end_loc.shape
     G = np.zeros((nb_shots, nb_raster_points, nb_dimension), dtype=np.float32)
     for i in range(nb_shots):
-        start = n_ramp_down[i,0]
-        G[i, : start] = np.linspace(
+        start = n_ramp_down[i, 0]
+        G[i, :start] = np.linspace(
             start_gradients[i], gi[i], n_ramp_down[i], endpoint=False, axis=-1
         )
-        if n_plateau[i, d] > 0:
+        if n_plateau[i] > 0:
             G[i, start : start + n_plateau[i, 0]] = gi[i]
-            start += n_plateau[i, 0]
+            start += n_plateau[i]
         G[i, start : start + n_ramp_up[i, 0]] = np.linspace(
             gi[i], end_gradients[i], n_ramp_up[i, 0], axis=-1, endpoint=False
         )