uvisbox.Modules.UncertaintyTube.uncertainty_tubes_mesh
======================================================

.. py:module:: uvisbox.Modules.UncertaintyTube.uncertainty_tubes_mesh




Module Contents
---------------

.. py:function:: expcos(x, e)

.. py:function:: expsin(x, e)

.. py:function:: compute_alignment_scores(reference, target, shifts)

   Compute alignment scores for all possible shifts of target relative to reference.

   :param reference: Reference point set (shape: n_points × num_dims)
   :type reference: np.ndarray
   :param target: Target point set to align (shape: n_points × num_dims)
   :type target: np.ndarray
   :param shifts: Array of shift values to try
   :type shifts: np.ndarray

   :returns: Scores for each shift (lower is better)
   :rtype: np.ndarray


.. py:function:: apply_circular_alignment(points, best_shift, best_is_reversed)

   Apply circular alignment transformation to a set of points based on the calculated
   shift and orientation.

   :param points (np.ndarray): Points to transform (shape: n_points × num_dims)
   :param best_shift (int): Number of positions to shift
   :param best_is_reversed (bool): Whether to reverse point order

   :returns: * *aligned (np.ndarray)* -- Transformed points
             * *point_correspondence_map (np.ndarray)* -- Index mapping from original to transformed points


.. py:function:: circular_align_min_twist(points_ref, points_target, stride=1)

   Aligns two sets of points forming closed loops with minimal twist.

   :param points_ref (np.ndarray): Reference point set (shape: n_points × num_dims)
   :param points_target (np.ndarray): Target point set to align (shape: n_points × num_dims)
   :param stride (int): Stride for sampling subset of points (for efficiency)

   :returns: * *aligned_points (np.ndarray)* -- Aligned target points
             * *correspondence_map (np.ndarray)* -- Index mapping from original to aligned points


.. py:function:: calculate_mesh_dimensions(n_steps, n_seeds, resolution)

   Calculate dimensions needed for mesh arrays.


.. py:function:: align_cross_sections(ellipsoids, seed_idx, n_steps, resolution)

   Align cross-sections to minimize twisting for a given seed.


.. py:function:: uncertainty_tubes_mesh(summary_statistics, resolution=20, e_proj=1, sym=False, n_jobs=1)

   Generate the 3D mesh for uncertainty tubes.

   :param summary_statistics (dict): Dictionary containing "mean_trajectory", "eigen_values", and "eigen_vectors".
   :param resolution (int: Number of points to sample on each cross-section boundary. Defaults to 20.
   :param optional): Number of points to sample on each cross-section boundary. Defaults to 20.
   :param e_proj (float: Exponent controlling the superellipse shape. e_proj=1 creates a standard ellipse.
                         Defaults to 1.
   :param optional): Exponent controlling the superellipse shape. e_proj=1 creates a standard ellipse.
                     Defaults to 1.
   :param sym (bool: If True, forces the superellipse to be symmetric. Defaults to False.
   :param optional): If True, forces the superellipse to be symmetric. Defaults to False.
   :param n_jobs (int: Number of parallel jobs to use. If n_jobs=1, uses sequential processing.
                       Defaults to 1.
   :param optional): Number of parallel jobs to use. If n_jobs=1, uses sequential processing.
                     Defaults to 1.

   :returns:

             - "vertices" (np.ndarray): Tube mesh vertices.
             - "faces" (np.ndarray): Triangle indices.
             - "uv_coords" (np.ndarray): UV coordinates for texture mapping.
   :rtype: dict