revert to private methods

Author: j-c-c

src/aspire/abinitio/__init__.py

@@ -3,10 +3,10 @@
 # isort: off
 from .commonline_utils import (
     JSync,
-    cl_angles_to_ind,
-    estimate_third_rows,
-    complete_third_row_to_rot,
-    estimate_inplane_rotations,
+    _cl_angles_to_ind,
+    _estimate_third_rows,
+    _complete_third_row_to_rot,
+    _estimate_inplane_rotations,
     g_sync,
 )
 from .commonline_sdp import CommonlineSDP

src/aspire/abinitio/commonline_c2.py

@@ -7,8 +7,8 @@
     CLOrient3D,
     JSync,
     SyncVotingMixin,
-    complete_third_row_to_rot,
-    estimate_third_rows,
+    _complete_third_row_to_rot,
+    _estimate_third_rows,
 )
 from aspire.utils import J_conjugate, Rotation, all_pairs
 
@@ -225,7 +225,7 @@ def estimate_rotations(self):
         viis = np.vstack((np.eye(3, dtype=self.dtype),) * self.n_img).reshape(
             self.n_img, 3, 3
         )
-        vis = estimate_third_rows(vijs, viis)
+        vis = _estimate_third_rows(vijs, viis)
 
         logger.info("Estimating in-plane rotations and rotations matrices.")
         Ris = self._estimate_inplane_rotations(vis, Rijs, Rijgs)
@@ -302,7 +302,7 @@ def _estimate_inplane_rotations(self, vis, Rijs, Rijgs):
         H = np.zeros((self.n_img, self.n_img), dtype=complex)
         # Step 1: Construct all rotation matrices Ris_tilde whose third rows are equal to
         # the corresponding third rows vis.
-        Ris_tilde = complete_third_row_to_rot(vis)
+        Ris_tilde = _complete_third_row_to_rot(vis)
 
         pairs = all_pairs(self.n_img)
         for idx, (i, j) in enumerate(pairs):

src/aspire/abinitio/commonline_c3_c4.py

@@ -7,8 +7,8 @@
     CLOrient3D,
     JSync,
     SyncVotingMixin,
-    estimate_inplane_rotations,
-    estimate_third_rows,
+    _estimate_inplane_rotations,
+    _estimate_third_rows,
 )
 from aspire.operators import PolarFT
 from aspire.utils import J_conjugate, Rotation, all_pairs, anorm, trange
@@ -108,10 +108,10 @@ def estimate_rotations(self):
         vijs, viis = self._global_J_sync(vijs, viis)
 
         logger.info("Estimating third rows of rotation matrices.")
-        vis = estimate_third_rows(vijs, viis)
+        vis = _estimate_third_rows(vijs, viis)
 
         logger.info("Estimating in-plane rotations and rotations matrices.")
-        Ris = estimate_inplane_rotations(self, vis)
+        Ris = _estimate_inplane_rotations(self, vis)
 
         self.rotations = Ris
 

src/aspire/abinitio/commonline_cn.py

@@ -6,10 +6,10 @@
 from aspire.abinitio import (
     CLOrient3D,
     JSync,
-    cl_angles_to_ind,
-    complete_third_row_to_rot,
-    estimate_inplane_rotations,
-    estimate_third_rows,
+    _cl_angles_to_ind,
+    _complete_third_row_to_rot,
+    _estimate_inplane_rotations,
+    _estimate_third_rows,
 )
 from aspire.operators import PolarFT
 from aspire.utils import (
@@ -115,10 +115,10 @@ def estimate_rotations(self):
         vijs, viis = self._global_J_sync(vijs, viis)
 
         logger.info("Estimating third rows of rotation matrices.")
-        vis = estimate_third_rows(vijs, viis)
+        vis = _estimate_third_rows(vijs, viis)
 
         logger.info("Estimating in-plane rotations and rotations matrices.")
-        Ris = estimate_inplane_rotations(self, vis)
+        Ris = _estimate_inplane_rotations(self, vis)
 
         self.rotations = Ris
 
@@ -349,8 +349,8 @@ def relative_rots_to_cl_indices(relative_rots, n_theta):
         c1s = np.array((-relative_rots[:, 1, 2], relative_rots[:, 0, 2])).T
         c2s = np.array((relative_rots[:, 2, 1], -relative_rots[:, 2, 0])).T
 
-        c1s = cl_angles_to_ind(c1s, n_theta)
-        c2s = cl_angles_to_ind(c2s, n_theta)
+        c1s = _cl_angles_to_ind(c1s, n_theta)
+        c2s = _cl_angles_to_ind(c2s, n_theta)
 
         inds = np.where(c1s >= n_theta // 2)
         c1s[inds] -= n_theta // 2
@@ -382,7 +382,7 @@ def generate_candidate_rots(n, equator_threshold, order, degree_res, seed):
             while counter < n:
                 third_row = randn(3)
                 third_row /= anorm(third_row, axes=(-1,))
-                Ri_tilde = complete_third_row_to_rot(third_row)
+                Ri_tilde = _complete_third_row_to_rot(third_row)
 
                 # Exclude candidates that represent equator images. Equator candidates
                 # induce collinear self-common-lines, which always have perfect correlation.

src/aspire/abinitio/commonline_utils.py

@@ -18,7 +18,7 @@
 logger = logging.getLogger(__name__)
 
 
-def estimate_third_rows(vijs, viis):
+def _estimate_third_rows(vijs, viis):
     """
     Find the third row of each rotation matrix given a collection of matrices
     representing the outer products of the third rows from each rotation matrix.
@@ -68,7 +68,7 @@ def estimate_third_rows(vijs, viis):
     return vis
 
 
-def estimate_inplane_rotations(cl_class, vis):
+def _estimate_inplane_rotations(cl_class, vis):
     """
     Estimate the rotation matrices for each image by constructing arbitrary rotation matrices
     populated with the given third rows, vis, and then rotating by an appropriate in-plane rotation.
@@ -89,7 +89,7 @@ def estimate_inplane_rotations(cl_class, vis):
 
     # Step 1: Construct all rotation matrices Ri_tildes whose third rows are equal to
     # the corresponding third rows vis.
-    Ri_tildes = complete_third_row_to_rot(vis)
+    Ri_tildes = _complete_third_row_to_rot(vis)
 
     # Step 2: Construct all in-plane rotation matrices, R_theta_ijs.
     max_angle = (360 // order) * order
@@ -146,8 +146,8 @@ def estimate_inplane_rotations(cl_class, vis):
                 c2s = np.array([[U[2, 1], -U[2, 0]] for U in Us])
 
                 # Convert from angles to indices.
-                c1s = cl_angles_to_ind(c1s, n_theta)
-                c2s = cl_angles_to_ind(c2s, n_theta)
+                c1s = _cl_angles_to_ind(c1s, n_theta)
+                c2s = _cl_angles_to_ind(c2s, n_theta)
 
                 # Perform correlation, corrs is shape n_shifts x len(theta_ijs).
                 corrs = np.array(
@@ -197,7 +197,7 @@ def estimate_inplane_rotations(cl_class, vis):
         return Ris
 
 
-def complete_third_row_to_rot(r3):
+def _complete_third_row_to_rot(r3):
     """
     Construct rotation matrices whose third rows are equal to the given row vectors.
     For vector r3 = [a, b, c], where [a, b, c] != [0, 0, 1], we return the matrix
@@ -246,7 +246,7 @@ def complete_third_row_to_rot(r3):
     return rots
 
 
-def cl_angles_to_ind(cl_angles, n_theta):
+def _cl_angles_to_ind(cl_angles, n_theta):
     thetas = np.arctan2(cl_angles[:, 1], cl_angles[:, 0])
 
     # Shift from [-pi,pi] to [0,2*pi).

tests/test_orient_symmetric.py

@@ -7,9 +7,9 @@
     CLSymmetryC2,
     CLSymmetryC3C4,
     CLSymmetryCn,
-    cl_angles_to_ind,
-    complete_third_row_to_rot,
-    estimate_third_rows,
+    _cl_angles_to_ind,
+    _complete_third_row_to_rot,
+    _estimate_third_rows,
     g_sync,
 )
 from aspire.abinitio.commonline_cn import MeanOuterProductEstimator
@@ -494,7 +494,7 @@ def test_estimate_third_rows(dtype):
 
     # Estimate third rows from outer products.
     # Due to factorization of V, these might be negated third rows.
-    vis = estimate_third_rows(vijs, viis)
+    vis = _estimate_third_rows(vijs, viis)
 
     # Check if all-close up to difference of sign
     ground_truth = np.sign(gt_vis[0, 0]) * gt_vis
@@ -512,7 +512,7 @@ def test_complete_third_row(dtype):
     r3[0] = np.array([0, 0, 1], dtype=dtype)
 
     # Generate rotations.
-    R = complete_third_row_to_rot(r3)
+    R = _complete_third_row_to_rot(r3)
 
     # Assert that first rotation is the identity matrix.
     assert np.allclose(R[0], np.eye(3, dtype=dtype))
@@ -643,6 +643,6 @@ def _gt_cl_c2(n_theta, rots_gt):
                 U = Ri.T @ g @ Rj
                 c1 = np.array([-U[1, 2], U[0, 2]])
                 c2 = np.array([U[2, 1], -U[2, 0]])
-                clmatrix_gt[idx, i, j] = cl_angles_to_ind(c1[np.newaxis, :], n_theta)
-                clmatrix_gt[idx, j, i] = cl_angles_to_ind(c2[np.newaxis, :], n_theta)
+                clmatrix_gt[idx, i, j] = _cl_angles_to_ind(c1[np.newaxis, :], n_theta)
+                clmatrix_gt[idx, j, i] = _cl_angles_to_ind(c2[np.newaxis, :], n_theta)
     return clmatrix_gt