From f1ccf3d305e402063ad89036149823fbb73cd9c6 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Fri, 22 Aug 2025 11:01:04 -0400
Subject: [PATCH 1/4] move estimate_third_rows to util file

---
 src/aspire/abinitio/__init__.py         |  1 +
 src/aspire/abinitio/commonline_c2.py    |  4 +-
 src/aspire/abinitio/commonline_c3_c4.py | 53 +-----------------------
 src/aspire/abinitio/commonline_utils.py | 55 +++++++++++++++++++++++++
 src/aspire/utils/__init__.py            |  1 +
 tests/test_orient_symmetric.py          | 12 +++---
 6 files changed, 68 insertions(+), 58 deletions(-)
 create mode 100644 src/aspire/abinitio/commonline_utils.py

diff --git a/src/aspire/abinitio/__init__.py b/src/aspire/abinitio/__init__.py
index fe91b322ad..a7acb5fc6a 100644
--- a/src/aspire/abinitio/__init__.py
+++ b/src/aspire/abinitio/__init__.py
@@ -1,6 +1,7 @@
 from .commonline_base import CLOrient3D
 
 # isort: off
+from .commonline_utils import estimate_third_rows
 from .commonline_sdp import CommonlineSDP
 from .commonline_lud import CommonlineLUD
 from .commonline_irls import CommonlineIRLS
diff --git a/src/aspire/abinitio/commonline_c2.py b/src/aspire/abinitio/commonline_c2.py
index 6bf6cf99ed..538c71cc56 100644
--- a/src/aspire/abinitio/commonline_c2.py
+++ b/src/aspire/abinitio/commonline_c2.py
@@ -3,7 +3,7 @@
 import numpy as np
 from scipy.linalg import eigh
 
-from aspire.abinitio import CLSymmetryC3C4
+from aspire.abinitio import CLSymmetryC3C4, estimate_third_rows
 from aspire.utils import J_conjugate, Rotation, all_pairs
 
 logger = logging.getLogger(__name__)
@@ -224,7 +224,7 @@ def estimate_rotations(self):
         viis = np.vstack((np.eye(3, dtype=self.dtype),) * self.n_img).reshape(
             self.n_img, 3, 3
         )
-        vis = self._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)
diff --git a/src/aspire/abinitio/commonline_c3_c4.py b/src/aspire/abinitio/commonline_c3_c4.py
index 0170d8b88f..13fd9dc4d3 100644
--- a/src/aspire/abinitio/commonline_c3_c4.py
+++ b/src/aspire/abinitio/commonline_c3_c4.py
@@ -3,7 +3,7 @@
 import numpy as np
 from numpy.linalg import eigh, norm, svd
 
-from aspire.abinitio import CLOrient3D, SyncVotingMixin
+from aspire.abinitio import CLOrient3D, SyncVotingMixin, estimate_third_rows
 from aspire.operators import PolarFT
 from aspire.utils import (
     J_conjugate,
@@ -110,7 +110,7 @@ def estimate_rotations(self):
         vijs, viis = self._global_J_sync(vijs, viis)
 
         logger.info("Estimating third rows of rotation matrices.")
-        vis = self._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)
@@ -209,55 +209,6 @@ def _global_J_sync(self, vijs, viis):
                 viis[i] = vii_J
         return vijs, viis
 
-    def _estimate_third_rows(self, 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.
-
-        :param vijs: An (n-choose-2)x3x3 array where each 3x3 slice holds the third rows
-        outer product of the rotation matrices Ri and Rj.
-
-        :param viis: An n_imgx3x3 array where the i'th 3x3 slice holds the outer product of
-        the third row of Ri with itself.
-
-        :param order: The underlying molecular symmetry.
-
-        :return: vis, An n_imgx3 matrix whose i'th row is the third row of the rotation matrix Ri.
-        """
-
-        n_img = self.n_img
-
-        # Build matrix V whose (i,j)-th block of size 3x3 holds the outer product vij
-        V = np.zeros((n_img, n_img, 3, 3), dtype=vijs.dtype)
-
-        # All pairs (i,j) where i<j
-        pairs = all_pairs(n_img)
-
-        # Populate upper triangle of V with vijs and lower triangle with vjis, where vji = vij^T.
-        for idx, (i, j) in enumerate(pairs):
-            V[i, j] = vijs[idx]
-            V[j, i] = vijs[idx].T
-
-        # Populate diagonal of V with viis
-        for i, vii in enumerate(viis):
-            V[i, i] = vii
-
-        # Permute axes and reshape to (3 * n_img, 3 * n_img).
-        V = np.swapaxes(V, 1, 2).reshape(3 * n_img, 3 * n_img)
-
-        # In a clean setting V is of rank 1 and its eigenvector is the concatenation
-        # of the third rows of all rotation matrices.
-        # In the noisy setting we use the eigenvector corresponding to the leading eigenvalue
-        val, vec = eigh(V)
-        lead_idx = np.argmax(val)
-        lead_vec = vec[:, lead_idx]
-
-        # We decompose the leading eigenvector and normalize to obtain the third rows, vis.
-        vis = lead_vec.reshape((n_img, 3))
-        vis /= anorm(vis, axes=(-1,))[:, np.newaxis]
-
-        return vis
-
     def _estimate_inplane_rotations(self, vis):
         """
         Estimate the rotation matrices for each image by constructing arbitrary rotation matrices
diff --git a/src/aspire/abinitio/commonline_utils.py b/src/aspire/abinitio/commonline_utils.py
new file mode 100644
index 0000000000..4a0e88bd5b
--- /dev/null
+++ b/src/aspire/abinitio/commonline_utils.py
@@ -0,0 +1,55 @@
+import numpy as np
+from numpy.linalg import eigh
+
+from aspire.utils.matrix import anorm
+from aspire.utils.misc import all_pairs
+
+
+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.
+
+    :param vijs: An (n-choose-2)x3x3 array where each 3x3 slice holds the third rows
+    outer product of the rotation matrices Ri and Rj.
+
+    :param viis: An n_imgx3x3 array where the i'th 3x3 slice holds the outer product of
+    the third row of Ri with itself.
+
+    :param order: The underlying molecular symmetry.
+
+    :return: vis, An n_imgx3 matrix whose i'th row is the third row of the rotation matrix Ri.
+    """
+
+    n_img = viis.shape[0]
+
+    # Build matrix V whose (i,j)-th block of size 3x3 holds the outer product vij
+    V = np.zeros((n_img, n_img, 3, 3), dtype=vijs.dtype)
+
+    # All pairs (i,j) where i<j
+    pairs = all_pairs(n_img)
+
+    # Populate upper triangle of V with vijs and lower triangle with vjis, where vji = vij^T.
+    for idx, (i, j) in enumerate(pairs):
+        V[i, j] = vijs[idx]
+        V[j, i] = vijs[idx].T
+
+    # Populate diagonal of V with viis
+    for i, vii in enumerate(viis):
+        V[i, i] = vii
+
+    # Permute axes and reshape to (3 * n_img, 3 * n_img).
+    V = np.swapaxes(V, 1, 2).reshape(3 * n_img, 3 * n_img)
+
+    # In a clean setting V is of rank 1 and its eigenvector is the concatenation
+    # of the third rows of all rotation matrices.
+    # In the noisy setting we use the eigenvector corresponding to the leading eigenvalue
+    val, vec = eigh(V)
+    lead_idx = np.argmax(val)
+    lead_vec = vec[:, lead_idx]
+
+    # We decompose the leading eigenvector and normalize to obtain the third rows, vis.
+    vis = lead_vec.reshape((n_img, 3))
+    vis /= anorm(vis, axes=(-1,))[:, np.newaxis]
+
+    return vis
diff --git a/src/aspire/utils/__init__.py b/src/aspire/utils/__init__.py
index ae896ebeb8..ae781d823f 100644
--- a/src/aspire/utils/__init__.py
+++ b/src/aspire/utils/__init__.py
@@ -1,4 +1,5 @@
 from .types import complex_type, real_type, utest_tolerance  # isort:skip
+
 from .coor_trans import (  # isort:skip
     mean_aligned_angular_distance,
     cart2pol,
diff --git a/tests/test_orient_symmetric.py b/tests/test_orient_symmetric.py
index 9ab63459df..aa44fcfdfb 100644
--- a/tests/test_orient_symmetric.py
+++ b/tests/test_orient_symmetric.py
@@ -3,7 +3,12 @@
 from numpy import pi, random
 from numpy.linalg import det, norm
 
-from aspire.abinitio import CLSymmetryC2, CLSymmetryC3C4, CLSymmetryCn
+from aspire.abinitio import (
+    CLSymmetryC2,
+    CLSymmetryC3C4,
+    CLSymmetryCn,
+    estimate_third_rows,
+)
 from aspire.abinitio.commonline_cn import MeanOuterProductEstimator
 from aspire.source import Simulation
 from aspire.utils import (
@@ -479,17 +484,14 @@ def test_global_J_sync(n_img, dtype):
 
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
 def test_estimate_third_rows(dtype):
-    L = 16
     n_img = 20
-    order = 3  # test not dependent on order
-    _, orient_est = source_orientation_objs(n_img, L, order, dtype)
 
     # Build outer products vijs, viis, and get ground truth third rows.
     vijs, viis, gt_vis = build_outer_products(n_img, dtype)
 
     # Estimate third rows from outer products.
     # Due to factorization of V, these might be negated third rows.
-    vis = orient_est._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

From b7ba1a434e5b357778082aa48fca3ca6d012d2aa Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 25 Aug 2025 09:13:43 -0400
Subject: [PATCH 2/4] migrate estimate_inplane_rotations,
 complete_third_row_to_rot to commonline utils.

---
 src/aspire/abinitio/__init__.py         |   7 +-
 src/aspire/abinitio/commonline_c2.py    |   8 +-
 src/aspire/abinitio/commonline_c3_c4.py | 212 +-----------------------
 src/aspire/abinitio/commonline_cn.py    |   8 +-
 src/aspire/abinitio/commonline_utils.py | 204 ++++++++++++++++++++++-
 tests/test_orient_symmetric.py          |  12 +-
 6 files changed, 229 insertions(+), 222 deletions(-)

diff --git a/src/aspire/abinitio/__init__.py b/src/aspire/abinitio/__init__.py
index a7acb5fc6a..3685479732 100644
--- a/src/aspire/abinitio/__init__.py
+++ b/src/aspire/abinitio/__init__.py
@@ -1,7 +1,12 @@
 from .commonline_base import CLOrient3D
 
 # isort: off
-from .commonline_utils import estimate_third_rows
+from .commonline_utils import (
+    cl_angles_to_ind,
+    estimate_third_rows,
+    complete_third_row_to_rot,
+    estimate_inplane_rotations,
+)
 from .commonline_sdp import CommonlineSDP
 from .commonline_lud import CommonlineLUD
 from .commonline_irls import CommonlineIRLS
diff --git a/src/aspire/abinitio/commonline_c2.py b/src/aspire/abinitio/commonline_c2.py
index 538c71cc56..52b63cc9e8 100644
--- a/src/aspire/abinitio/commonline_c2.py
+++ b/src/aspire/abinitio/commonline_c2.py
@@ -3,7 +3,11 @@
 import numpy as np
 from scipy.linalg import eigh
 
-from aspire.abinitio import CLSymmetryC3C4, estimate_third_rows
+from aspire.abinitio import (
+    CLSymmetryC3C4,
+    complete_third_row_to_rot,
+    estimate_third_rows,
+)
 from aspire.utils import J_conjugate, Rotation, all_pairs
 
 logger = logging.getLogger(__name__)
@@ -301,7 +305,7 @@ 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 = self._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):
diff --git a/src/aspire/abinitio/commonline_c3_c4.py b/src/aspire/abinitio/commonline_c3_c4.py
index 13fd9dc4d3..bd9522e865 100644
--- a/src/aspire/abinitio/commonline_c3_c4.py
+++ b/src/aspire/abinitio/commonline_c3_c4.py
@@ -3,7 +3,12 @@
 import numpy as np
 from numpy.linalg import eigh, norm, svd
 
-from aspire.abinitio import CLOrient3D, SyncVotingMixin, estimate_third_rows
+from aspire.abinitio import (
+    CLOrient3D,
+    SyncVotingMixin,
+    estimate_inplane_rotations,
+    estimate_third_rows,
+)
 from aspire.operators import PolarFT
 from aspire.utils import (
     J_conjugate,
@@ -12,7 +17,6 @@
     all_triplets,
     anorm,
     cyclic_rotations,
-    tqdm,
     trange,
 )
 from aspire.utils.random import randn
@@ -113,7 +117,7 @@ def estimate_rotations(self):
         vis = estimate_third_rows(vijs, viis)
 
         logger.info("Estimating in-plane rotations and rotations matrices.")
-        Ris = self._estimate_inplane_rotations(vis)
+        Ris = estimate_inplane_rotations(self, vis)
 
         self.rotations = Ris
 
@@ -209,140 +213,6 @@ def _global_J_sync(self, vijs, viis):
                 viis[i] = vii_J
         return vijs, viis
 
-    def _estimate_inplane_rotations(self, 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.
-
-        :param vis: An n_imgx3 array where the i'th row holds the estimate for the third row of
-        the i'th rotation matrix.
-
-        :return: Rotation matrices Ris and in-plane rotation matrices R_thetas, both size n_imgx3x3.
-        """
-        pf = self.pf
-        n_img = self.n_img
-        n_theta = self.n_theta
-        max_shift_1d = self.max_shift
-        shift_step = self.shift_step
-        order = self.order
-        degree_res = self.degree_res
-
-        # Step 1: Construct all rotation matrices Ri_tildes whose third rows are equal to
-        # the corresponding third rows vis.
-        Ri_tildes = self._complete_third_row_to_rot(vis)
-
-        # Step 2: Construct all in-plane rotation matrices, R_theta_ijs.
-        max_angle = (360 // order) * order
-        theta_ijs = np.arange(0, max_angle, degree_res) * np.pi / 180
-        R_theta_ijs = Rotation.about_axis("z", theta_ijs, dtype=self.dtype).matrices
-
-        # Step 3: Compute the correlation over all shifts.
-        # Generate shifts.
-        r_max = pf.shape[-1]
-        shifts, shift_phases, _ = self._generate_shift_phase_and_filter(
-            r_max, max_shift_1d, shift_step
-        )
-        n_shifts = len(shifts)
-
-        # Q is the n_img x n_img  Hermitian matrix defined by Q = q*q^H,
-        # where q = (exp(i*order*theta_0), ..., exp(i*order*theta_{n_img-1}))^H,
-        # and theta_i in [0, 2pi/order) is the in-plane rotation angle for the i'th image.
-        Q = np.zeros((n_img, n_img), dtype=complex)
-
-        # Reconstruct the full polar Fourier for use in correlation. self.pf only consists of
-        # rays in the range [180, 360), with shape (n_img, n_theta//2, n_rad-1).
-        pf = PolarFT.half_to_full(pf)
-
-        # Normalize rays.
-        pf /= norm(pf, axis=-1)[..., np.newaxis]
-
-        n_pairs = n_img * (n_img - 1) // 2
-        with tqdm(total=n_pairs) as pbar:
-            idx = 0
-            # Note: the ordering of i and j in these loops should not be changed as
-            # they correspond to the ordered tuples (i, j), for i<j.
-            for i in range(n_img):
-                pf_i = pf[i]
-
-                # Generate shifted versions of images.
-                pf_i_shifted = np.array(
-                    [pf_i * shift_phase for shift_phase in shift_phases]
-                )
-
-                Ri_tilde = Ri_tildes[i]
-
-                for j in range(i + 1, n_img):
-                    pf_j = pf[j]
-
-                    Rj_tilde = Ri_tildes[j]
-
-                    # Compute all possible rotations between the i'th and j'th images.
-                    Us = np.array(
-                        [
-                            Ri_tilde.T @ R_theta_ij @ Rj_tilde
-                            for R_theta_ij in R_theta_ijs
-                        ]
-                    )
-
-                    # Find the angle between common lines induced by the rotations.
-                    c1s = np.array([[-U[1, 2], U[0, 2]] for U in Us])
-                    c2s = np.array([[U[2, 1], -U[2, 0]] for U in Us])
-
-                    # Convert from angles to indices.
-                    c1s = self.cl_angles_to_ind(c1s, n_theta)
-                    c2s = self.cl_angles_to_ind(c2s, n_theta)
-
-                    # Perform correlation, corrs is shape n_shifts x len(theta_ijs).
-                    corrs = np.array(
-                        [
-                            np.dot(pf_i_shift[c1], np.conj(pf_j[c2]))
-                            for pf_i_shift in pf_i_shifted
-                            for c1, c2 in zip(c1s, c2s)
-                        ]
-                    )
-
-                    # Reshape to group by shift and symmetric order.
-                    corrs = corrs.reshape((n_shifts, order, len(theta_ijs) // order))
-
-                    # For each pair of lines we take the maximum correlation over all shifts.
-                    corrs = np.max(np.real(corrs), axis=0)
-
-                    # corrs[i] is the set of correlations for theta_ij in [2pi * i / order, 2pi * (i + 1) / order).
-                    # Due to symmetry, each corrs[i] represents correlations over identical pairs of lines.
-                    # With that in mind, we average over corrs[i] and find the max correlation.
-                    # This produces an index corresponding to theta_ij in the range [0, 2pi/order).
-                    corrs = np.mean(np.real(corrs), axis=0)
-                    max_idx_corr = np.argmax(corrs)
-
-                    theta_ij = degree_res * max_idx_corr * np.pi / 180
-
-                    Q[i, j] = np.exp(-1j * order * theta_ij)
-
-                    pbar.update()
-
-                    idx += 1
-
-            # Populate the lower triangle and diagonal of Q.
-            # Diagonals are 1 since e^{i*0}=1.
-            Q += np.conj(Q).T + np.eye(n_img)
-
-            # Q is a rank-1 Hermitian matrix.
-            eig_vals, eig_vecs = eigh(Q)
-            leading_eig_vec = eig_vecs[:, -1]
-            logger.info(
-                f"Top 3 eigenvalues of Q (rank-1) are {str(eig_vals[-3:][::-1])}."
-            )
-
-            # Calculate R_thetas.
-            R_thetas = Rotation.about_axis(
-                "z", np.angle(leading_eig_vec ** (1 / order))
-            )
-
-            # Form rotation matrices Ris.
-            Ris = R_thetas @ Ri_tildes
-
-            return Ris
-
     #################################################
     # Secondary Methods for computing outer product #
     #################################################
@@ -742,74 +612,6 @@ def _signs_times_v(self, vijs, vec):
 
         return new_vec
 
-    ###########################################
-    # Secondary Methods fo In-Plane Rotations #
-    ###########################################
-    @staticmethod
-    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
-        with rows r1, r2, r3, given by:
-
-        r1 = 1/sqrt(a^2 + b^2)[b, -a, 0],
-        r2 = 1/sqrt(a^2 + b^2)[ac, bc, -(a^2 + b^2)].
-
-        :param r3: A nx3 array where each row vector has norm 1.
-        :return: An nx3x3 array of rotation matrices whose third rows are r3.
-        """
-
-        # Handle singleton vector.
-        singleton = False
-        if r3.shape == (3,):
-            r3 = np.expand_dims(r3, axis=0)
-            singleton = True
-
-        # Initialize output rotation matrices.
-        rots = np.zeros((len(r3), 3, 3), dtype=r3.dtype)
-
-        # Populate 3rd rows.
-        rots[:, 2] = r3
-
-        # Mask for third rows that do not coincide with the z-axis.
-        mask = np.linalg.norm(r3 - [0, 0, 1], axis=1) >= 1e-5
-
-        # If the third row coincides with the z-axis we return the identity matrix.
-        rots[~mask] = np.eye(3, dtype=r3.dtype)
-
-        # 'norm_12' is non-zero since r3 does not coincide with the z-axis.
-        norm_12 = np.sqrt(r3[mask, 0] ** 2 + r3[mask, 1] ** 2)
-
-        # Populate 1st rows with vector orthogonal to row 3.
-        rots[mask, 0, 0] = r3[mask, 1] / norm_12
-        rots[mask, 0, 1] = -r3[mask, 0] / norm_12
-
-        # Populate 2nd rows such that r3 = r1 x r2
-        rots[mask, 1, 0] = r3[mask, 0] * r3[mask, 2] / norm_12
-        rots[mask, 1, 1] = r3[mask, 1] * r3[mask, 2] / norm_12
-        rots[mask, 1, 2] = -norm_12
-
-        if singleton:
-            rots = rots.reshape(3, 3)
-
-        return rots
-
-    @staticmethod
-    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).
-        thetas = np.mod(thetas, 2 * np.pi)
-
-        # linear scale from [0,2*pi) to [0,n_theta).
-        ind = np.mod(np.round(thetas / (2 * np.pi) * n_theta), n_theta).astype(int)
-
-        # Return scalar for single value.
-        if ind.size == 1:
-            ind = ind.flat[0]
-
-        return ind
-
     @staticmethod
     def g_sync(rots, order, rots_gt):
         """
diff --git a/src/aspire/abinitio/commonline_cn.py b/src/aspire/abinitio/commonline_cn.py
index a1440cadc3..e0d69cb086 100644
--- a/src/aspire/abinitio/commonline_cn.py
+++ b/src/aspire/abinitio/commonline_cn.py
@@ -3,7 +3,7 @@
 import numpy as np
 from numpy.linalg import norm
 
-from aspire.abinitio import CLSymmetryC3C4
+from aspire.abinitio import CLSymmetryC3C4, cl_angles_to_ind, complete_third_row_to_rot
 from aspire.operators import PolarFT
 from aspire.utils import (
     J_conjugate,
@@ -298,8 +298,8 @@ 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 = CLSymmetryC3C4.cl_angles_to_ind(c1s, n_theta)
-        c2s = CLSymmetryC3C4.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
@@ -331,7 +331,7 @@ 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 = CLSymmetryC3C4._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.
diff --git a/src/aspire/abinitio/commonline_utils.py b/src/aspire/abinitio/commonline_utils.py
index 4a0e88bd5b..bfd1e5ce5f 100644
--- a/src/aspire/abinitio/commonline_utils.py
+++ b/src/aspire/abinitio/commonline_utils.py
@@ -1,8 +1,12 @@
+import logging
+
 import numpy as np
-from numpy.linalg import eigh
+from numpy.linalg import eigh, norm
+
+from aspire.operators import PolarFT
+from aspire.utils import Rotation, all_pairs, anorm, tqdm
 
-from aspire.utils.matrix import anorm
-from aspire.utils.misc import all_pairs
+logger = logging.getLogger(__name__)
 
 
 def estimate_third_rows(vijs, viis):
@@ -53,3 +57,197 @@ def estimate_third_rows(vijs, viis):
     vis /= anorm(vis, axes=(-1,))[:, np.newaxis]
 
     return 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.
+
+    :cl_class: A commonlines class instance.
+    :param vis: An n_imgx3 array where the i'th row holds the estimate for the third row of
+    the i'th rotation matrix.
+
+    :return: Rotation matrices Ris and in-plane rotation matrices R_thetas, both size n_imgx3x3.
+    """
+    pf = cl_class.pf
+    n_img = cl_class.n_img
+    n_theta = cl_class.n_theta
+    max_shift_1d = cl_class.max_shift
+    shift_step = cl_class.shift_step
+    order = cl_class.order
+    degree_res = cl_class.degree_res
+
+    # 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)
+
+    # Step 2: Construct all in-plane rotation matrices, R_theta_ijs.
+    max_angle = (360 // order) * order
+    theta_ijs = np.arange(0, max_angle, degree_res) * np.pi / 180
+    R_theta_ijs = Rotation.about_axis("z", theta_ijs, dtype=cl_class.dtype).matrices
+
+    # Step 3: Compute the correlation over all shifts.
+    # Generate shifts.
+    r_max = pf.shape[-1]
+    shifts, shift_phases, _ = cl_class._generate_shift_phase_and_filter(
+        r_max, max_shift_1d, shift_step
+    )
+    n_shifts = len(shifts)
+
+    # Q is the n_img x n_img  Hermitian matrix defined by Q = q*q^H,
+    # where q = (exp(i*order*theta_0), ..., exp(i*order*theta_{n_img-1}))^H,
+    # and theta_i in [0, 2pi/order) is the in-plane rotation angle for the i'th image.
+    Q = np.zeros((n_img, n_img), dtype=complex)
+
+    # Reconstruct the full polar Fourier for use in correlation. cl_class.pf only consists of
+    # rays in the range [180, 360), with shape (n_img, n_theta//2, n_rad-1).
+    pf = PolarFT.half_to_full(pf)
+
+    # Normalize rays.
+    pf /= norm(pf, axis=-1)[..., np.newaxis]
+
+    n_pairs = n_img * (n_img - 1) // 2
+    with tqdm(total=n_pairs) as pbar:
+        idx = 0
+        # Note: the ordering of i and j in these loops should not be changed as
+        # they correspond to the ordered tuples (i, j), for i<j.
+        for i in range(n_img):
+            pf_i = pf[i]
+
+            # Generate shifted versions of images.
+            pf_i_shifted = np.array(
+                [pf_i * shift_phase for shift_phase in shift_phases]
+            )
+
+            Ri_tilde = Ri_tildes[i]
+
+            for j in range(i + 1, n_img):
+                pf_j = pf[j]
+
+                Rj_tilde = Ri_tildes[j]
+
+                # Compute all possible rotations between the i'th and j'th images.
+                Us = np.array(
+                    [Ri_tilde.T @ R_theta_ij @ Rj_tilde for R_theta_ij in R_theta_ijs]
+                )
+
+                # Find the angle between common lines induced by the rotations.
+                c1s = np.array([[-U[1, 2], U[0, 2]] for U in Us])
+                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)
+
+                # Perform correlation, corrs is shape n_shifts x len(theta_ijs).
+                corrs = np.array(
+                    [
+                        np.dot(pf_i_shift[c1], np.conj(pf_j[c2]))
+                        for pf_i_shift in pf_i_shifted
+                        for c1, c2 in zip(c1s, c2s)
+                    ]
+                )
+
+                # Reshape to group by shift and symmetric order.
+                corrs = corrs.reshape((n_shifts, order, len(theta_ijs) // order))
+
+                # For each pair of lines we take the maximum correlation over all shifts.
+                corrs = np.max(np.real(corrs), axis=0)
+
+                # corrs[i] is the set of correlations for theta_ij in [2pi * i / order, 2pi * (i + 1) / order).
+                # Due to symmetry, each corrs[i] represents correlations over identical pairs of lines.
+                # With that in mind, we average over corrs[i] and find the max correlation.
+                # This produces an index corresponding to theta_ij in the range [0, 2pi/order).
+                corrs = np.mean(np.real(corrs), axis=0)
+                max_idx_corr = np.argmax(corrs)
+
+                theta_ij = degree_res * max_idx_corr * np.pi / 180
+
+                Q[i, j] = np.exp(-1j * order * theta_ij)
+
+                pbar.update()
+
+                idx += 1
+
+        # Populate the lower triangle and diagonal of Q.
+        # Diagonals are 1 since e^{i*0}=1.
+        Q += np.conj(Q).T + np.eye(n_img)
+
+        # Q is a rank-1 Hermitian matrix.
+        eig_vals, eig_vecs = eigh(Q)
+        leading_eig_vec = eig_vecs[:, -1]
+        logger.info(f"Top 3 eigenvalues of Q (rank-1) are {str(eig_vals[-3:][::-1])}.")
+
+        # Calculate R_thetas.
+        R_thetas = Rotation.about_axis("z", np.angle(leading_eig_vec ** (1 / order)))
+
+        # Form rotation matrices Ris.
+        Ris = R_thetas @ Ri_tildes
+
+        return Ris
+
+
+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
+    with rows r1, r2, r3, given by:
+
+    r1 = 1/sqrt(a^2 + b^2)[b, -a, 0],
+    r2 = 1/sqrt(a^2 + b^2)[ac, bc, -(a^2 + b^2)].
+
+    :param r3: A nx3 array where each row vector has norm 1.
+    :return: An nx3x3 array of rotation matrices whose third rows are r3.
+    """
+
+    # Handle singleton vector.
+    singleton = False
+    if r3.shape == (3,):
+        r3 = np.expand_dims(r3, axis=0)
+        singleton = True
+
+    # Initialize output rotation matrices.
+    rots = np.zeros((len(r3), 3, 3), dtype=r3.dtype)
+
+    # Populate 3rd rows.
+    rots[:, 2] = r3
+
+    # Mask for third rows that do not coincide with the z-axis.
+    mask = np.linalg.norm(r3 - [0, 0, 1], axis=1) >= 1e-5
+
+    # If the third row coincides with the z-axis we return the identity matrix.
+    rots[~mask] = np.eye(3, dtype=r3.dtype)
+
+    # 'norm_12' is non-zero since r3 does not coincide with the z-axis.
+    norm_12 = np.sqrt(r3[mask, 0] ** 2 + r3[mask, 1] ** 2)
+
+    # Populate 1st rows with vector orthogonal to row 3.
+    rots[mask, 0, 0] = r3[mask, 1] / norm_12
+    rots[mask, 0, 1] = -r3[mask, 0] / norm_12
+
+    # Populate 2nd rows such that r3 = r1 x r2
+    rots[mask, 1, 0] = r3[mask, 0] * r3[mask, 2] / norm_12
+    rots[mask, 1, 1] = r3[mask, 1] * r3[mask, 2] / norm_12
+    rots[mask, 1, 2] = -norm_12
+
+    if singleton:
+        rots = rots.reshape(3, 3)
+
+    return rots
+
+
+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).
+    thetas = np.mod(thetas, 2 * np.pi)
+
+    # linear scale from [0,2*pi) to [0,n_theta).
+    ind = np.mod(np.round(thetas / (2 * np.pi) * n_theta), n_theta).astype(int)
+
+    # Return scalar for single value.
+    if ind.size == 1:
+        ind = ind.flat[0]
+
+    return ind
diff --git a/tests/test_orient_symmetric.py b/tests/test_orient_symmetric.py
index aa44fcfdfb..d7c4c4716f 100644
--- a/tests/test_orient_symmetric.py
+++ b/tests/test_orient_symmetric.py
@@ -7,6 +7,8 @@
     CLSymmetryC2,
     CLSymmetryC3C4,
     CLSymmetryCn,
+    cl_angles_to_ind,
+    complete_third_row_to_rot,
     estimate_third_rows,
 )
 from aspire.abinitio.commonline_cn import MeanOuterProductEstimator
@@ -509,7 +511,7 @@ def test_complete_third_row(dtype):
     r3[0] = np.array([0, 0, 1], dtype=dtype)
 
     # Generate rotations.
-    R = CLSymmetryC3C4._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))
@@ -640,10 +642,6 @@ 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] = CLSymmetryC3C4.cl_angles_to_ind(
-                    c1[np.newaxis, :], n_theta
-                )
-                clmatrix_gt[idx, j, i] = CLSymmetryC3C4.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

From 89dfbdb02d72ccb249855d501186f634bc0c9028 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Mon, 25 Aug 2025 11:29:18 -0400
Subject: [PATCH 3/4] migrate syncmatrix_ij_vote_3n to SyncVotingMixin. Remove
 C3C4 implimentation.

---
 src/aspire/abinitio/commonline_c3_c4.py  | 29 ---------------------
 src/aspire/abinitio/commonline_sync3n.py | 31 -----------------------
 src/aspire/abinitio/sync_voting.py       | 32 ++++++++++++++++++++++++
 3 files changed, 32 insertions(+), 60 deletions(-)

diff --git a/src/aspire/abinitio/commonline_c3_c4.py b/src/aspire/abinitio/commonline_c3_c4.py
index bd9522e865..af74dc6f6c 100644
--- a/src/aspire/abinitio/commonline_c3_c4.py
+++ b/src/aspire/abinitio/commonline_c3_c4.py
@@ -369,35 +369,6 @@ def _estimate_all_Rijs_c3_c4(self, clmatrix):
 
         return Rijs
 
-    def _syncmatrix_ij_vote_3n(self, clmatrix, i, j, k_list, n_theta):
-        """
-        Compute the (i,j) rotation block of the synchronization matrix using voting method
-
-        Given the common lines matrix `clmatrix`, a list of images specified in k_list
-        and the number of common lines n_theta, find the (i, j) rotation block Rij.
-
-        :param clmatrix: The common lines matrix
-        :param i: The i image
-        :param j: The j image
-        :param k_list: The list of images for the third image for voting algorithm
-        :param n_theta: The number of points in the theta direction (common lines)
-        :return: The (i,j) rotation block of the synchronization matrix
-        """
-        _, good_k = self._vote_ij(clmatrix, n_theta, i, j, k_list)
-
-        rots = self._rotratio_eulerangle_vec(clmatrix, i, j, good_k, n_theta)
-
-        if rots is not None:
-            rot_mean = np.mean(rots, 0)
-
-        else:
-            # This is for the case that images i and j correspond to the same
-            # viewing direction and differ only by in-plane rotation.
-            # We set to zero as in the Matlab code.
-            rot_mean = np.zeros((3, 3))
-
-        return rot_mean
-
     def _local_J_sync_c3_c4(self, Rijs, Riis):
         """
         Estimate viis and vijs. In order to estimate vij = vi @ vj.T, it is necessary for Rii, Rjj,
diff --git a/src/aspire/abinitio/commonline_sync3n.py b/src/aspire/abinitio/commonline_sync3n.py
index 841f9dfceb..39f57ab978 100644
--- a/src/aspire/abinitio/commonline_sync3n.py
+++ b/src/aspire/abinitio/commonline_sync3n.py
@@ -969,37 +969,6 @@ def _estimate_all_Rijs_host(self, clmatrix):
 
         return Rijs
 
-    def _syncmatrix_ij_vote_3n(self, clmatrix, i, j, k_list, n_theta):
-        """
-        Compute the (i,j) rotation block of the synchronization matrix using voting method
-
-        Given the common lines matrix `clmatrix`, a list of images specified in k_list
-        and the number of common lines n_theta, find the (i, j) rotation block Rij.
-
-        :param clmatrix: The common lines matrix
-        :param i: The i image
-        :param j: The j image
-        :param k_list: The list of images for the third image for voting algorithm
-        :param n_theta: The number of points in the theta direction (common lines)
-        :return: The (i,j) rotation block of the synchronization matrix
-        """
-        alphas, good_k = self._vote_ij(clmatrix, n_theta, i, j, k_list, sync=True)
-
-        angles = np.zeros(3)
-
-        if alphas is not None:
-            angles[0] = clmatrix[i, j] * 2 * np.pi / n_theta + np.pi / 2
-            angles[1] = np.mean(alphas)
-            angles[2] = -np.pi / 2 - clmatrix[j, i] * 2 * np.pi / n_theta
-            rot = Rotation.from_euler(angles).matrices
-
-        else:
-            # This is for the case that images i and j correspond to the same
-            # viewing direction and differ only by in-plane rotation.
-            # We set to zero as in the Matlab code.
-            rot = np.zeros((3, 3))
-
-        return rot
 
     #######################################
     # Secondary Methods for Global J Sync #
diff --git a/src/aspire/abinitio/sync_voting.py b/src/aspire/abinitio/sync_voting.py
index 651ba35c5e..b866f1e8ff 100644
--- a/src/aspire/abinitio/sync_voting.py
+++ b/src/aspire/abinitio/sync_voting.py
@@ -13,6 +13,38 @@ class SyncVotingMixin(object):
     which are shared by CLSynVoting and CLSymmetryC3C4
     """
 
+    def _syncmatrix_ij_vote_3n(self, clmatrix, i, j, k_list, n_theta):
+        """
+        Compute the (i,j) rotation block of the synchronization matrix using voting method
+
+        Given the common lines matrix `clmatrix`, a list of images specified in k_list
+        and the number of common lines n_theta, find the (i, j) rotation block Rij.
+
+        :param clmatrix: The common lines matrix
+        :param i: The i image
+        :param j: The j image
+        :param k_list: The list of images for the third image for voting algorithm
+        :param n_theta: The number of points in the theta direction (common lines)
+        :return: The (i,j) rotation block of the synchronization matrix
+        """
+        alphas, good_k = self._vote_ij(clmatrix, n_theta, i, j, k_list, sync=True)
+
+        angles = np.zeros(3)
+
+        if alphas is not None:
+            angles[0] = clmatrix[i, j] * 2 * np.pi / n_theta + np.pi / 2
+            angles[1] = np.mean(alphas)
+            angles[2] = -np.pi / 2 - clmatrix[j, i] * 2 * np.pi / n_theta
+            rot = Rotation.from_euler(angles).matrices
+
+        else:
+            # This is for the case that images i and j correspond to the same
+            # viewing direction and differ only by in-plane rotation.
+            # We set to zero as in the Matlab code.
+            rot = np.zeros((3, 3))
+
+        return rot
+
     def _rotratio_eulerangle_vec(self, clmatrix, i, j, good_k, n_theta):
         """
         Compute the rotation that takes image i to image j

From 06283962f6ea54a094a770f332b6f95f2c779ec5 Mon Sep 17 00:00:00 2001
From: Josh Carmichael <carmichael@princeton.edu>
Date: Tue, 26 Aug 2025 15:01:35 -0400
Subject: [PATCH 4/4] remove unused import

---
 src/aspire/abinitio/commonline_sync3n.py | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/src/aspire/abinitio/commonline_sync3n.py b/src/aspire/abinitio/commonline_sync3n.py
index 39f57ab978..25bfd63015 100644
--- a/src/aspire/abinitio/commonline_sync3n.py
+++ b/src/aspire/abinitio/commonline_sync3n.py
@@ -7,15 +7,7 @@
 from scipy.optimize import curve_fit
 
 from aspire.abinitio import CLOrient3D, SyncVotingMixin
-from aspire.utils import (
-    J_conjugate,
-    Rotation,
-    all_pairs,
-    nearest_rotations,
-    random,
-    tqdm,
-    trange,
-)
+from aspire.utils import J_conjugate, all_pairs, nearest_rotations, random, tqdm, trange
 from aspire.utils.matlab_compat import stable_eigsh
 
 logger = logging.getLogger(__name__)
@@ -969,7 +961,6 @@ def _estimate_all_Rijs_host(self, clmatrix):
 
         return Rijs
 
-
     #######################################
     # Secondary Methods for Global J Sync #
     #######################################