Alignment/centering: changed API

Signed-off-by: Nicola VIGANO <nicola.vigano@esrf.fr>
cicwi · Mar 26, 2024 · 8606a69 · 8606a69
1 parent 849e165
commit 8606a69
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Showing 3 changed files with 13 additions and 15 deletions.
diff --git a/corrct/alignment/centering.py b/corrct/alignment/centering.py
@@ -17,7 +17,7 @@
 
 
 class RecenterVolume:
-    """Volume recentering class."""
+    """Volume re-centering class."""
 
     def __init__(
         self, proj_geom: models.ProjectionGeometry, angles_rad: Union[NDArray, ArrayLike], precision: int = 2
@@ -40,9 +40,7 @@ def _apply_displacement_vu(self, shifts_vu: NDArray, displacemenet_zyx: NDArray)
         shifts_vu_corrs = self.prj_geom.project_displacement_to_detector(displacemenet_zyx)
         return np.around(shifts_vu + shifts_vu_corrs, decimals=self.precision)
 
-    def recenter_to(
-        self, shifts_vu: Union[ArrayLike, NDArray], volume: NDArray, com_ref_zyx: Union[ArrayLike, NDArray]
-    ) -> NDArray:
+    def to_com(self, shifts_vu: Union[ArrayLike, NDArray], volume: NDArray, com_ref_zyx: Union[ArrayLike, NDArray]) -> NDArray:
         """Recenter to a given center-of-mass (CoM).
 
         Parameters
@@ -63,7 +61,7 @@ def recenter_to(
         displacemenet_zyx = com_ref_zyx - com_rec_zyx
         return self._apply_displacement_vu(shifts_vu, displacemenet_zyx)
 
-    def recenter_as(self, shifts_vu: NDArray, volume: NDArray, reference: NDArray, method: str = "com") -> NDArray:
+    def as_reference(self, shifts_vu: NDArray, volume: NDArray, reference: NDArray, method: str = "com") -> NDArray:
         """Recenter with respect to a given volume.
 
         Parameters
@@ -89,7 +87,7 @@ def recenter_as(self, shifts_vu: NDArray, volume: NDArray, reference: NDArray, m
         """
         if method.lower() == "com":
             com_ref_zyx = post_proc.com(reference)
-            return self.recenter_to(shifts_vu, volume, com_ref_zyx)
+            return self.to_com(shifts_vu, volume, com_ref_zyx)
         elif method.lower() == "xc":
             displacemenet_zyx = fitting.fit_shifts_zyx_xc(reference, volume, decimals=self.precision)
             return self._apply_displacement_vu(shifts_vu, displacemenet_zyx)

diff --git a/examples/alignment/example_01_pre-alignment.py b/examples/alignment/example_01_pre-alignment.py
@@ -102,9 +102,9 @@ def cm2inch(x: Union[float, Sequence[float], NDArray]) -> Sequence[float]:
     rec_noise_pre, _ = solver(A, data_test, iterations=ITERATIONS, **solver_opts)
 
 # Recentering the reconstructions on the phantom's center-of-mass -> moving the shifts accordingly
-theo_rot_axis = recenter.recenter_to(THEO_ROT_AXIS, rec_noise_theocor, com_ph_yx)
-cor = recenter.recenter_to(cor, rec_noise_precor, com_ph_yx)
-shifts_u_pre = recenter.recenter_to(shifts_u_pre, rec_noise_pre, com_ph_yx)
+theo_rot_axis = recenter.to_com(THEO_ROT_AXIS, rec_noise_theocor, com_ph_yx)
+cor = recenter.to_com(cor, rec_noise_precor, com_ph_yx)
+shifts_u_pre = recenter.to_com(shifts_u_pre, rec_noise_pre, com_ph_yx)
 
 # Reconstructing again, with centered shifts
 with cct.projectors.ProjectorUncorrected(ph.shape, angles_rad, theo_rot_axis) as A:

diff --git a/tests/test_alignment.py b/tests/test_alignment.py
@@ -155,12 +155,12 @@ def test_pre_alignment(add_noise: bool, theo_rot_axis: float = -1.25):
     recenter = cct.alignment.RecenterVolume(prj_geom, angles_rad)
 
     # Re-centering the reconstructions on the phantom's center-of-mass -> moving the shifts accordingly
-    shifts_u_pre = recenter.recenter_to(shifts_u_pre, rec_noise_pre, com_ph_yx)
+    shifts_u_pre = recenter.to_com(shifts_u_pre, rec_noise_pre, com_ph_yx)
 
     if debug:
         theo_rot_axis_per_angle = np.ones_like(angles_rad) * theo_rot_axis
-        theo_rot_axis_per_angle = recenter.recenter_to(theo_rot_axis_per_angle, rec_noise_theocor, com_ph_yx)
-        cor = recenter.recenter_to(cor, rec_noise_precor, com_ph_yx)
+        theo_rot_axis_per_angle = recenter.to_com(theo_rot_axis_per_angle, rec_noise_theocor, com_ph_yx)
+        cor = recenter.to_com(cor, rec_noise_precor, com_ph_yx)
 
         print(f"{theo_shifts = }")
         print(f"{shifts_u_pre = }")
@@ -246,14 +246,14 @@ def test_pre_alignment_3d(add_noise: bool, theo_rot_axis: float = -1.25):
     recenter = cct.alignment.RecenterVolume(prj_geom, angles_rad)
 
     # Re-centering the reconstructions on the phantom's center-of-mass -> moving the shifts accordingly
-    shifts_vu_pre = recenter.recenter_to(shifts_vu_pre, rec_noise_xc, com_ph_yx)
+    shifts_vu_pre = recenter.to_com(shifts_vu_pre, rec_noise_xc, com_ph_yx)
     if debug:
         theo_rot_axis_per_angle = cct.models.combine_shifts_vu(
             np.zeros_like(angles_rad), np.ones_like(angles_rad) * theo_rot_axis
         )
-        theo_rot_axis_per_angle = recenter.recenter_to(theo_rot_axis_per_angle, rec_noise_theocor, com_ph_yx)
+        theo_rot_axis_per_angle = recenter.to_com(theo_rot_axis_per_angle, rec_noise_theocor, com_ph_yx)
         cor_pre = cct.models.combine_shifts_vu(np.zeros_like(angles_rad), np.ones_like(angles_rad) * cor_pre)
-        cor_pre = recenter.recenter_to(cor_pre, rec_noise_precor, com_ph_yx)
+        cor_pre = recenter.to_com(cor_pre, rec_noise_precor, com_ph_yx)
 
         print(f"{theo_shifts_vu = }")
         print(f"{shifts_vu_pre = }")